EXPERIMENTAL CHARACTERIZATION AND NUMERICAL … › sk › ...Thesis_Kassegne_Lab.pdf · MODELING OF THERMAL AND ELECTROCHEMISTRY EFFECTS IN 3D BIONANOELECTRONICS PLATFORM _____ A

EXPERIMENTAL CHARACTERIZATION AND NUMERICAL

MODELING OF THERMAL AND ELECTROCHEMISTRY EFFECTS IN

3D BIONANOELECTRONICS PLATFORM

_______________

A Thesis

Presented to the

Faculty of

San Diego State University

_______________

In Partial Fulfillment

of the Requirements for the Degree

Master of Science

in

Bioengineering

_______________

by

Neha Chowdhry

Fall 2012

iii

Copyright © 2012

by

Neha Chowdhry

All Rights Reserved

iv

DEDICATION

I would like to dedicate this master’s thesis to my parents, Ashok Chowdhry and Ina

Chowdhry for their unconditional support with my studies. I thank them for helping me to

improve myself through all walks of my life, and I would have never gotten here had it not

been for their guidance and support.

I would also like to dedicate this thesis to my friend and companion, Ashish Gaikwad,

who has been a pillar of strength to me in innumerable ways, and I thank him for his

immeasurable love, patience and steadfast support at all times.

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Thinkers do not accept the inevitable; they turn their efforts towards changing it.

--Sri Sri Paramahansa Yogananda

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ABSTRACT OF THE THESIS

Experimental Characterization and Numerical Modeling of Thermal and Electrochemistry Effects in 3D Bionanoelectronics

Platform by

Neha Chowdhry Master of Science in Bioengineering

San Diego State University, 2012

This study investigates through experimentation and numerical modeling, the degree of variation in pH and temperature for 3D gold electrode-based bionanoelectronics platform. The pH and thermal sensitivity of these electrodes gives an estimate of the optimum environmental conditions for efficient operation of DNA wires on the proposed architecture. This study demonstrates, through numerical modeling and experimental analysis, a drop in pH at the anode and increase in basicity at the cathode in response to an externally applied DC bias. On similar lines, the phenomenon of Joule heating of the 3D gold electrodes is also described to illustrate variations in temperature to change in voltage.

Additional parameters such as the influence of spacing between adjacent electrodes on variations in pH are determined, and it is verified that greater the spacing between adjacent electrodes in a microarray, lesser is the degree of variation in pH. For this purpose, a number of chips were microfabricated with different spacing dimensions between them to determine its influence on pH variation over a wide range of data points. Keywords: Bionanoelectronics, Joule heating, Histidine, Negative Photolithography, DNA hybridization, DC bias, Protonation.

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TABLE OF CONTENTS

PAGE

ABSTRACT ............................................................................................................................. vi

LIST OF TABLES ................................................................................................................... xi

LIST OF FIGURES ................................................................................................................ xii

ACKNOWLEDGEMENTS .....................................................................................................xv

CHAPTER

1 INTRODUCTION .........................................................................................................1

1.1 Motivation for Research ....................................................................................2

1.2 Organization of Thesis .......................................................................................5

2 LITERATURE SURVEY ..............................................................................................6

2.1 Bionanoelectronics .............................................................................................6

2.2 Bionanoelectronics Platform ..............................................................................8

2.3 Characterization of Bionanoelectronic Architecture .........................................9

2.3.1 Quantitative Characterization of 3D Microelectrode Arrays ..................11

2.3.2 Manipulation of Localized Environmental Effects .................................12

3 DESIGN & MICROFABRICATION OF 3D BIONANOELECTRONIC CHIP ............................................................................................................................14

3.1 Chip Design & Mask Layout ...........................................................................15

3.1.1 Design I Mask .........................................................................................15

3.1.2 Design II Mask (“Mithras” Feature) .......................................................16

3.1.3 Design III Mask (“Indra” Feature) ..........................................................16

3.2 3-D Negative Photolithography Protocol .........................................................17

3.2.1 Wafer Preparation ...................................................................................17

3.2.2 Dehydration Bake ...................................................................................17

3.2.3 Photoresist Coat ......................................................................................19

3.2.4 Soft Bake .................................................................................................19

3.2.5 Expose .....................................................................................................19

3.2.6 Post-Bake ................................................................................................21

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3.2.7 Gold Sputtering .......................................................................................21

3.2.8 Development /Stripping ..........................................................................22

3.2.9 Imaging ...................................................................................................22

4 ELECTROCHEMISTRY CHARACTERIZATION ...................................................24

4.1 pH-Based Characterization of 3D Metal Electrodes ........................................24

4.1.1 Description of the Equipment Used ........................................................24

4.1.1.1 pH Meter (JE671-T) .......................................................................24

4.1.1.2 Reference Electrode (DRI-REF 450) .............................................25

4.1.1.3 Beetrode pH Electrode (NMPH2B) ...............................................25

4.1.1.4 Z-BEE-CAL ...................................................................................26

4.1.2 Calibration Process .................................................................................27

4.1.2.1 Calibration of pH Meter .................................................................27

4.1.2.2 Calibration of Z-BEE-CAL ............................................................27

4.1.2.3 Calibration of Beetrode ..................................................................28

4.1.3 Main Experimental Procedure ................................................................29

4.1.4 Experiment with Design I Chip ..............................................................30

4.1.4.1 Wire Bonding .................................................................................30

4.1.4.2 Main Experimental Set-up .............................................................30

4.1.4.3 Results & Discussion .....................................................................31

4.1.5 Experiment with Mithras ........................................................................31



4.1.6 Experiment with Indra ............................................................................34



4.1.7 Discussion of Results ..............................................................................35

4.2 Experimental Analysis Of The Temporal Variation Of pH .............................36

4.3 Numerical Modeling of 3D Electrodes For pH Characterization ....................37

4.3.1 Model Geometry .....................................................................................38

4.3.2 Description of the Physics Used .............................................................40

4.3.2.1 Electrostatic System .......................................................................40

4.3.2.2 Generation and Migration of H+ and OH- ions ..............................40

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4.3.2.3 Protonation and De-Protonation of Zwitterionic Histidine and Migration of His+ ions .............................................................43

4.3.3 Solution of Numerical Model .................................................................43

4.3.3.1 Surface Concentration of H+ ions ..................................................44

4.3.3.2 Surface Concentration of His+ ions ................................................45

4.3.3.3 Surface Concentration of Hisz ........................................................45

4.3.4 Results & Discussion ..............................................................................46

4.4 Comparison of Results .....................................................................................48

5 TEMPERATURE CHARACTERIZATION ...............................................................50

5.1 Temperature-Based Characterization of 3D Metal Electrodes ........................50

5.1.1 Experiment with Design I Chip ..............................................................50



5.1.2 Experiment with Mithras ........................................................................52



5.1.3 Experiment with Indra ............................................................................53



5.2 Numerical Modeling of 3D Electrodes for Temperature Characterization ...............................................................................................56

5.2.1 Description of the Physics Used .............................................................56

5.2.1.1 Electrostatic System .......................................................................57

5.2.1.2 General heat transfer ......................................................................57

5.2.2. Solution of Numerical Model ................................................................57

5.2.2.1 Surface Temperature ......................................................................57

5.2.2.2 Dependence of Surface Temperature Distribution on Thermal Conductivity ....................................................................57

5.2.2.3 Resistive Heating ...........................................................................58

5.2.2.4 Electric field Distribution ..............................................................58

5.2.3 Results & Discussion ..............................................................................58

5.2.4 Comparison of Results ............................................................................62

6 CONCLUSION ............................................................................................................63

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6.1 Future Reseach Goals ......................................................................................63

6.2 Future Research ...............................................................................................64

REFERENCES ........................................................................................................................65

APPENDIX

A PARAMETRIC ANALYSIS FOR MODELING VARIATIONS IN PH ...................68

B PARAMETRIC ANALYSIS FOR MODELING VARIATIONS IN TEMPERATURE ........................................................................................................73

C NUMERICAL MODELING OF DNA HYBRIDIZATION .......................................76

D PARAMETRIC ANALYSIS FOR MODELING HYBRIDIZATION OF DNA ON PROPOSED ARCHITECTURE .................................................................81

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LIST OF TABLES

PAGE

Table 3.1. Summary of the Chip Designs Used for Experimentation .....................................18

Table 4.1. List of Specifications for JE671T pH Meter ...........................................................25

Table 4.2. List of Specifications for Beetrode .........................................................................26

Table 4.3. Calibration Results ..................................................................................................28

Table 4.4. Experimental Results for Design I-pH Variation ...................................................32

Table 4.5. Experimental Results for Design II-pH Variation (Mithras) ..................................33

Table 4.6. Experimental Results for Design III-pH Variation (Indra) .....................................35

Table 4.7. Experimental Results for Temporal Variation of pH ..............................................38

Table 4.8. Summary of the Boundary Conditions Used in the Numerical Model ...................41

Table 4.9. Simulation Results for Design II- pH Variation (Cathode) ....................................47

Table 4.10. Simulation Results for Design III-Results ............................................................48

Table 5.1. Experimental Results for Design I-Temperature ....................................................52

Table 5.2. Experimental Results for Design II-Temperature ...................................................54

Table 5.3. Experimental Results for Design III-Temperature .................................................55

Table 5.4. Summary of the Variation of Surface Temperature with Thermal .........................59

Table 5.5. Simulation Results for Design III-Temperature .....................................................62

Table C.1. Summary of the Boundary Conditions Used in the Numerical Model ..................79

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LIST OF FIGURES

PAGE

Figure 1.1. Performance of semiconductor technology. ............................................................2

Figure 1.2. DNA strand between gold metal atoms. ..................................................................3

Figure 1.3. An artist's depiction of the lipid-covered silicon nanowire device..........................3

Figure 1.4. Research roadmap, bionanoelectronics research group, SDSU. .............................4

Figure 2.1. Comparison of typical dimensions of several biological and nanomaterials. ................................................................................................................7

Figure 2.2. Direct covalent modification of carbon nanotubes and silicon nanowires with biological molecules. .............................................................................................8

Figure 2.3. Chemical structure of L-Histidine and Imidazole ring. .........................................11

Figure 2.4. SEM image of 3D C-MEMS microarray.. .............................................................12

Figure 2.5. (a) DEP forces v/s distance from the electrode surface in both 2D and 3D electrodes (b) Relationship between change in temperature and applied voltage. .........................................................................................................................13

Figure 3.1. SU-8 molecule. ......................................................................................................14

Figure 3.2. Image of the mask layout (left); Chip used for experimentation (right). ..............16

Figure 3.3. Design II Mask Layout and Mithras feature design. .............................................16

Figure 3.4. Design II Mask Layout and Indra feature design. .................................................17

Figure 3.5. Clean room station. ................................................................................................18

Figure 3.6. Spin coater. ............................................................................................................19

Figure 3.7. Hot plate. ...............................................................................................................20

Figure 3.8. OAI U.V. light source. ..........................................................................................20

Figure 3.9. Gold sputtering machine. .......................................................................................21

Figure 3.10. Ultrasonic bath. ....................................................................................................22

Figure 3.11. Images of the various features used for experimentation. ...................................23

Figure 4.1. Screen grab of JE671T pH meter. .........................................................................25

Figure 4.2. Images of Dri-Ref 450. ..........................................................................................25

Figure 4.3. Images of Beetrode. ...............................................................................................26

Figure 4.4. Image of the Z-BEE-CAL battery. ........................................................................26

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Figure 4.5. Experimental Beetrode set-up. ..............................................................................27

Figure 4.6. Ideal Nernstian plot. ..............................................................................................28

Figure 4.7. Calibration plot. .....................................................................................................29

Figure 4.8. Main experimental set-up for Gen I Chip. .............................................................31

Figure 4.9. Variation of pH with respect to voltage for Design I. ...........................................32

Figure 4.10. Main experimental set-up for Mithras. ................................................................33

Figure 4.11. Variation of pH with respect to voltage for Mithras. ..........................................34

Figure 4.12. Main experimental set-up for Indra. ....................................................................35

Figure 4.13. Variation of pH with respect to voltage for Indra. ..............................................36

Figure 4.14. Dependence of pH on spacing between the electrodes. ......................................36

Figure 4.15. Estimate of the total number of chips microfabricated for each design. .............37

Figure 4.16. Temporal variation of pH with respect to voltage. ..............................................37

Figure 4.17. Illustration of the Bionanoelectronics model. .....................................................39

Figure 4.18. Electrode geometry. .............................................................................................39

Figure 4.19. Distribution of H+ ions at the anode and cathode. ..............................................44

Figure 4.20. Temporal Variation of H+ ion concentration at 2 distinct points of the anode. ...........................................................................................................................44

Figure 4.21. Temporal Variation of H+ ion concentration at 2 distinct points of cathode. ........................................................................................................................45

Figure 4.22. Distribution of His+ ions at the anode and cathode. ...........................................45

Figure 4.23. Generation of His+ ions at anode. .......................................................................45

Figure 4.24. Generation of His+ ions at cathode. ....................................................................46

Figure 4.25. Distribution of zwitterionic Histidine along the anode and cathode. ..................46

Figure 4.26. Reduction of Hisz ions at anode. .........................................................................46

Figure 4.27. Temporal variation of pH with respect to Electric Potential. ..............................47

Figure 4.28. Temporal variation of pH at the cathode. ............................................................48

Figure 4.29. Comparison of the experimental and simulation results for the degree of variation in pH. ............................................................................................................49

Figure 5.1. Main experimental set-up for Gen I Chip. .............................................................51

Figure 5.2. Variation of temperature with respect to voltage. .................................................52

Figure 5.3. Main Experimental set-upapplied directly at the electrode. Moreover, the thermocouple is placed directly at the spacing between the electrodes for the subsequent experiments. ..............................................................................................53

Figure 5.4. Grabs of temperature readings recorded on the Thermocouple meter. .................54

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Figure 5.5. Main Experimental set-up. ....................................................................................55

Figure 5.6. Screen grabs of temperature readings recorded on the Thermocouple meter. ...........................................................................................................................56

Figure 5.7. Estimate of the total number of chips microfabricated for each design. ...............56

Figure 5.8. Surface temperature along the anode and cathode; zoomed-in view of the temperature distribution at the spacing. .......................................................................58

Figure 5.9. Variation of temperature with thermal conductivity. ............................................60

Figure 5.10. Resistive heating; zoomed-in view of the resistive heating at the spacing. ........60

Figure 5.11. Electric Field; zoomed-in view of the electric field at the spacing. ....................61

Figure 5.12. Temporal variation of temperature with respect to voltage. ................................61

Figure 5.13. Comparison of the experimental and simulation results for the degree of variation in temperature. ..............................................................................................62

Figure A.1. Subdomain settings-conductive media DC for pH. ..............................................69

Figure A.2. Boundary settings-conductive media DC for pH. ................................................69

Figure A.3. Subdomain settings-electrokinetic flow (H+). .....................................................70

Figure A.4. Boundary settings-electrokinetic flow (H+). ........................................................70

Figure A.5. Subdomain settings-electrokinetic flow (His+). ...................................................71

Figure A.6. Boundary settings-electrokinetic flow (His+). .....................................................71

Figure A.7. Subdomain settings-electrokinetic flow (HisZ). ...................................................72

Figure A.8. Boundary settings-electrokinetic flow (HisZ). .....................................................72

Figure B.1. Subdomain settings-conductive media dc for temperature. ..................................74

Figure B.2. Boundary settings-conductive media dc for temperature. ....................................74

Figure B.3. Subdomain settings - general heat transfer. ..........................................................75

Figure B.4. Boundary settings - general heat transfer. ............................................................75

Figure C.1. DNA Hybridization after 60s. ...............................................................................80

Figure C.2. Surface concentration of hybridized dsDNA. .......................................................80

Figure D.1. Subdomain settings-electrokinetic flow(ssDNA). ................................................82

Figure D.2. Boundary settings-electrokinetic flow(ssDNA). ..................................................82

Figure D.3. Subdomain settings-diffusion (HybDNA). ...........................................................83

Figure D.4. Boundary settings-diffusion (HybDNA). .............................................................83

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ACKNOWLEDGEMENTS

I thank Almighty God for giving me the courage and determination in conducting this

research study.

I extend my deepest gratitude to my thesis advisor, Dr. Sam Kassegne, for his

guidance, motivation and constant encouragement throughout this research, and for being

very tolerant to see me through. I thank him for his dedication in providing all the possible

resources and funds to complete this research.

Also, I would like to thank Dr. Steven Barlow for providing me access to the Electron

Microscope and Sputtering Machine facilities.

My special thanks goes to the MEMS Research group at San Diego State University

for their contribution and assistance to this project. I would like to show my gratitude to my

colleagues, Beejal Mehta and Nasim Wahidi for nailing down the photolithography process,

and helping me with the microfabrication of chips for experimentation purposes.

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CHAPTER 1

INTRODUCTION

New developments in technology continue to give rise to cutting-edge innovations in

engineering designs at micro and nano levels. One of the most promising areas of research is

at the junction between biology, nanotechnology and electronics and deals with the

technological applications of self-assembly systems in which molecules closely associate

with each other to form supra-molecular structures. This bottom-up self-assembly concept is

useful to engineer nano-scale functional units, which can further be used to design molecular

electronic devices.

The development of memory devices and microprocessors has enabled the

semiconductor technology to achieve remarkable growth. For example, the performance of

personal computers in early 1970s was only 0.1 million instructions per second (MIPS) as

shown in Figure 1.1 [1]. However, according to recent statistics, the computer performance

has exceeded 100 MIPS, which shows an improvement of more than 4 orders of magnitude

[2]. This has been possible due to the evolution of sub-micron and finer-pattern processes in

semiconductor technology, which has enabled the micro-fabrication of several sub-systems

on a single piece of silicon.

Miniaturization of semiconductor devices is giving rise to new opportunities in

biomedical research. Bioelectronics has the ability to impact areas like medicine, homeland

security, forensic sciences, and environmental protection, all of which are vital to the nation’s

economy and well-being. The artificial retina, which enables restoration of sight in people

with degenerative diseases of the retina, and recent development of implantable drug delivery

devices based on MEMS technology, illustrate these advancements [1]. Moreover, nanoscale

bioelectronics will be important in genomics and proteomics to determine the function and

role of proteins in cellular pathways.

According to a recent report, steady progress in bioelectronics can lead to the

development of improved methods and tools, while simultaneously reducing their costs, due

to the continuous exponential gains in functionality-per-unit-cost in nano-electronics, as

2

Figure 1.1. Performance of semiconductor technology. Source: Semiconductor Electronics Division. “A Framework for Bioelectronics Discovery and Innovation.” National Institute of Standards and Technology 2, no. 3 (2009): 211-212.

stated by Moore’s law [3]. Gordon Moore, from the Intel Corporation, formulated a law in

1965, now known as Moore’s Law, stating that the number of transistors on a chip would

double every 18 months. However, this trend has drastically changed from 2010 and the

doubling rate has dropped to every 4–5 years. DNA-based electronics has the potential to

extend beyond Moore’s Law, proclaiming the end of conventional microelectronics.

With the progress of Moore’s law, the number of semiconductor applications in life

sciences has also increased with time. A lot of effort has been put in to develop surface

chemistries that can be used to attach biological molecules to semiconductor substrates [4].

DNA recognition based on surface-bound DNA-functionalized polypyrrole molecules

(illustrated in Figure 1.2.[5]) and silicon nanowire devices (shown in Figure 1.3 [5]) is an

example [5].

1.1 MOTIVATION FOR RESEARCH

Bionanoelectronics constitutes a significant area of research carried out at Kassegne’s

MEMS Research lab at SDSU. Figure 1.4 illustrates the research work being pursued.

3

Figure 1.2. DNA strand between gold metal atoms. Source:Korri-Youssoufi, H., F. Garnier, P. Srivastava, P. Godillot, and A. Yassar. “Toward Bioelectronics: Specific DNA recognition based on an oligonucleotide-functionalized polypyrrole.” J Am Chem Soc 119 (1997): 7388-7389.

Figure 1.3. An artist's depiction of the lipid-covered silicon nanowire device. Source: Korri-Youssoufi, H., F. Garnier, P. Srivastava, P. Godillot, and A. Yassar. “Toward Bioelectronics: Specific DNA recognition based on an oligonucleotide-functionalized polypyrrole.” J Am Chem Soc 119 (1997): 7388-7389.

4

Figure 1.4. Research roadmap, bionanoelectronics research group, SDSU.

The characterization and experimental testing of the micro-chips based on the proposed

Bionanoelectronics architecture is important to successfully design bionanoelectronic

devices. Moreover, experimental analysis of the variations in pH and temperature on a sub-

micron scale has never been performed. To repeat and refine the experimental procedure,

analyze the wide range of data points with respect to specific parameters, and validate these

using finite element simulation software was the main motivation for this research.

This research summarizes the thermal and pH sensitivity of gold electrodes and their

significance as potential substrates for designing bionanoelectronic devices. Gold electrode is

commonly used in electronic architectures because of its stability and corrosion resistance

[2]. Moreover, L-Histidine is used as the electrolyte to analyze the influence of Histidine

protonation on variations in pH.

5

1.2 ORGANIZATION OF THESIS

This thesis is organized in the following sequence: Chapter 1 presents a basic

introduction to this research; Chapter 2 summarizes literature survey including the

significance of Bionanoelectronics, and characterization of the proposed Bio-microelectronic

architecture; Chapter 3 describes design and micro-fabrication procedures; Chapter 4

includes a detailed explanation of the experimental and simulation results for pH-based

characterization of the 3D gold electrodes, including a comparison between the experimental

and modeling results; Chapter 5 explains experimental and simulation results for

temperature-based characterization of 3D gold electrodes, together with a comparison of the

simulation and the experimental results; Chapter 6 provides essential conclusions drawn from

this research.

6

CHAPTER 2

LITERATURE SURVEY

Over the past few decades, a nearly exponential growth in the field of

microelectronics has been achieved, owing to the steady improvement in the performance of

silicon-based VLSI circuits by scaling down the device dimensions [6]. Additionally, top-

down micro-patterning techniques like photolithography have accelerated nanotechnology to

a point where system-process integration with bottom-up self-assembly is required. However,

maintaining this top down miniaturization trend is becoming difficult since this technology

requires a combination of instrumentation, clean-room environment, and materials whose

cost increases at a much faster pace, as compared to the incremental benefits obtained by

reduction in size [7, 8]. In contrast, the use of organic molecules as building blocks for the

fabrication of nano-scale devices is far more promising and is gradually gaining importance.

The bottom up approach uses chemical properties of single organic molecules to enable them

to self-organize into a useful conformation, wherein these molecules can be interconnected

by planar metallic nano-patterns to form precisely controlled nanostructures [8]. This

approach is capable of introducing nano-devices in parallel, which are much cheaper than

those developed using the top-down approach.

2.1 BIONANOELECTRONICS

Every cell uses a vast variety of proteins, ion channels, signaling molecules and

carriers to perform intricate functions in a living organism. However, being able to

incorporate these biological processes into man-made Nano-devices, at that level of

complexity, is yet to be accomplished [9].

To date, many devices have made rapid advancement towards practical realization of

this goal. First are a variety of biosensors that incorporate a biological recognition system

(bioreceptor) and a transducer, to quantify multiple analytes based on their recognition

interaction with the bioreceptor, which triggers an electrical signal measured by the

transducer [10]. An array of bioreceptors ranging from antibodies, proteins, micro-organisms,

7

nucleic acids (DNA), and enzymes have been used for the nano-fabrication of these

biosensor devices. Second are the genetically encoded intracellular sensors that are capable

of recording biochemical electrical potentials with remarkable special and temporal

resolution, based on fluorescent proteins [11]. Third are the bionanoelectronic circuits that

attempt to couple biological structures and nano-scale electronics in order to perform

complex functions. The discovery of nanowires and nanotubes has enabled researchers to

fabricate electronic interfaces with components of dimensions comparable to the size of

biological molecules [12-14]. Wang et al. constructed a SWNT-based field effect transistor

(FET) to monitor the neuronal activity of cells [15]. The FET device was developed using

photolithography, and then coated with single-walled carbon nanotubes for the real time

detection of molecules released from neurons and sensing neural activity. A comparison of

the typical dimensions of several bio and nanomaterials is shown in Figure 2.1 [9].

Figure 2.1. Comparison of typical dimensions of several biological and nanomaterials. Source: Cingolani, Roberto, Ross Rinaldi, Giuseppe Maruccio, and Adriana Biasco. ”Nanotechnology approaches to Self organized biomolecular devices.” Physica E: Low-dimensional systems and nanostructures 13, no. 2-3 (March 2002): 1229-1235.

As science continues to unfold improved materials, the ongoing research in

Bionanoelectronics can give rise to diagnostic devices, smart prosthetics, neural circuits, and

other innovative ways of interfacing with devices.

8

2.2 BIONANOELECTRONICS PLATFORM

Combining nanomaterials with biomolecules to develop functional bionanoelectronic

circuits is difficult because biomolecules function best in salty water, which however is not

ideal for the operation of electronic circuits. Graphite surfaces as in carbon nanotubes, silicon

oxide surfaces used in silicon nanowires, and gold surfaces of gold nanowires are the

commonly exploited platforms for construction of bionanoelectronic devices. All of these are

known to easily bind to biomolecules through strong π-π, hydrophobic or ionic interactions,

but at the same time, these strong forces can also alter the conformation of biomolecules

[16]. Thus, the substrate material is an important factor wile assembling biomolecules on

electronic architectures.

Several approaches have been tried to achieve a functional bionanoelectronic

platform. One of these is the high energy covalent modification of the graphite sidewalls of

carbon nanotubes by oxidation or fluorination. Biomolecules can then be covalently attached

to the oxidized surface of carbon nanotubes by EDAC coupling as depicted in Figure 2.2

[16]. Similarly, silicon nanowires with hydrogen terminals can be covalently functionalized

to achieve substrate-DNA coupling.

Figure 2.2. Direct covalent modification of carbon nanotubes and silicon nanowires with biological molecules. Source: Wang, C. W., C. Y. Pan, H. C. Wu, P. Y. Shih, C. C. Tsai, K. T. Liao, L. L. Lu, W. H. Hsieh, C. D. Chen, and Y. T. Chen.“Insitu Detection of Chromogranin a Released From Released From Living Neurons with a Single-Walled-Carbon-Nanotube Field-Effect Transistor.” Small 3 (2007): 1350-1355.

9

According to a recent research, single-stranded DNA (ssDNA) covering carbon

nanotubes with gold electrical contacts to the device, was used as a functionalization scheme

for the detection of DNA hybridization [17, 18]. Nanotubes and nanowires transistors

consisting of a nanowire attached between two lithographically developed electrodes on a

substrate surface are reported to have the most widespread use in bionanoelectronics. There

are several reasons for this: (a) they can operate in ionic solutions which are a suitable

environment for most biomolecules; (b) they provide firm connections between the micron-

scale active area of the device and the large-sized measurement equipment; (c) transistor gain

helps to amplify the weak signals generated by biomolecules during operation of the device.

[19, 20].

2.3 CHARACTERIZATION OF BIONANOELECTRONIC

ARCHITECTURE

The interface that associates biomolecules with microelectronic circuits should be

able to provide a suitable environment that would sustain the biological structure, and at the

same time enable efficient coupling between the biological and inorganic components. The

main aim of this thesis is to characterize the 3D metal electrodes used for attaching the DNA

wire on silicon substrate, so that it can enable accurate, sensitive and rapid DNA transport,

site selective concentration, and accelerated hybridization reactions. These processes are

governed by certain physical parameters like DC voltage, type and conductivity of the buffer

species. It is known that at any given current and voltage level, the mobility of DNA is

inversely proportional to the buffer conductivity. Therefore, hybridization of DNA occurs

only in the presence of low conductivity buffers, and at a certain range of pH and

temperature [21, 22].

Electronically active microchip-based nucleic acid arrays adopt electric field as the

driving force for transport, accumulation and hybridization of the nucleotide fragments. Such

bioelectronic devices have been extensively used for gene sequencing, molecular diagnostics,

gene profiling, pharmacogenomics, as well as forensic and genetic identification purposes

[20-22]. DNA microarrays are increasingly being used in biological sciences to enable

interpretation of data emerging from large-scale genome sequencing.

Low conductivity buffers are vital to accelerate the transport of nucleic acids by free

solution electrophoresis [23]. Moreover, these low-ionic strength buffers enable efficient

10

transport of oligonucleotides to specific sites, when exposed to a DC bias. In order to attain

low conductivity, zwitterionic buffers having no net charge near neutral pH are essential.

However, it has been observed that many zwitterionic buffers, which also have low

conductivity, like glycine, GABA, and beta-alanine, do not optimally shield the nucleic acid

phosphodiester backbone charges, due to which these buffers are not capable of hybridizing

DNA under passive conditions. These buffers therefore, do not support passive hybridization,

due to which electronic control allows promotes hybridization only at discreet sites [19-23].

Histidine is the buffer of choice for promoting DNA hybridization because of its low

conductivity of around 60µS/cm, and highly efficient buffering capacity. When exposed to a

DC bias, histidine has demonstrated the ability to buffer acidic conditions, which develop at

the anode owing to the dissociation of water and generation of H+ ions at the anode. The

buffering ability of histidine is a consequence of the protonation of zwitterionic histidine

given by the following chemical equilibrium reaction:

According to research done by Zhang et al. [24], since nucleic acids are strong

polyelectrolytes with negatively charged phosphodiester backbones, a positively charged

structure tends to accelerate the transport of nucleic acid molecules. The protonated histidine

ions have a net positive charge which then shield or diminishes repulsion between the DNA

strands, thereby promoting hybridization within a narrow pH range. The shorthands His+ and

Hisz are used for representing protonated histidine and zwitterionic histidine respectively.

The efficiency with which buffers support hybridization of DNA is also dependant

upon the nature of fun ctional groups present. This means that once the criteria for possessing

a buffering capacity within the hybridization window, and the resulting generation of a

positively charged species have been met, the hybridization process may also be influenced

by other functional groups. As shown in Figure 2.3 [24], The imidazole side-chain of

histidine is the primary source of buffering for histidine within a narrow pH range. Imidazole

is a weak base with pka value near neutrality. The excellent buffering capacity of histidine is

due to its ability to sustain a positive charge on both the imidazole ring an the primary amine

group.

11

Figure 2.3. Chemical structure of L-Histidine and Imidazole ring. Source: Heller, M. J. “DNA Microarray Technology: Devices, Systems, and Applications.” Ann. Rev. Biomed. Eng. 4 (2002) 129–153.

2.3.1 Quantitative Characterization of 3D Microelectrode Arrays

Rena et al. have investigated the electrochemical effect of flower-shaped micro

features that constitute an electrode [25]. The sharp tips on micro metal particles tend to

enhance the electric field capacity of the microarray consisting of Pt/Au bilayered electrode.

Due to the presence of a larger surface area and sharp edges, the capacitance of Au micro-

flower array was found to be 20 times larger than that of Au pitch-array electrode for a given

potential [26].

Chu et al. have designed and fabricated 3D silicon 10x10 micro electrode arrays

consisting of electrodes of 60μm height and 30μm width, covered with SiO2 isolation layer

for bio-neural applications. Existing researchers have shown that planar electrodes which are

only few microns thick cannot penetrate the tissue to facilitate recordings in deeper neurons,

and therefore 3D microelectrode arrays prove to be a good alternative [27].

Larsson has demonstrated the versatile manufacturability of polymer SU-8, and its

various applications in developing micro structures using MEMS fabrication techniques [28].

Lu et al. have characterized the electric field generated by 2D Au/Cr electrodes and

3D copper electrodes. According to their research, the electric field generated at 2D

electrodes decays exponentially with the distance from the electrode [29].

Wang et al. have succeeded in developing 3D C-MEMS micro electrodes with aspect

ratio of 10:1 by pyrolyzing SU-8, a negative photoresist as shown in Figure 2.4 [29, 30]. The

increase in volume as a result of increase in height results in higher capacitance in 3D

microarrays as compared to un-patterned carbon films.

Tay et al have performed electrical and thermal characterization of a dielectrophoretic

(DEP) chip with 3D microelectrodes for cell manipulation [31, 32]. They have demonstrated

12

Figure 2.4. SEM image of 3D C-MEMS microarray. Source: Huai-Yuan, Chu, Kuo Tzu-Ying, Chang Baowen, Lu Shao-Wei, Chiao Chuan-Chin and Fang Weileun. “Design and Fabrication of Novel 3D Multi-Electrode Array Using SOI Wafer.” Sensors and Actuators A: Physical, 130-131 (2006): 254-261.

through theoretical analysis that 3D electrodes tend to maintain constant DEP force in the

cross section of the fluidic device, whereas the efficiency of 2D planar electrode decreases

exponentially as shown in Figure 1.2. As the 3D electrodes possess higher trapping

efficiency, they can be used for high volume cell manipulation. They have also performed

numerical simulation (represented graphically in Figure 2.5. [35]) using ANSYS to show that

the variation in temperature with applied voltage is 8 to 10 times lower in 3D electrodes as

compared to planar electrodes.

2.3.2 Manipulation of Localized Environmental Effects

Variations in pH, salinity, ionic concentrations, and temperature are expected during

the self-assembly process of manufacturing DNA wires, and also during the operation of

DNA wires and interconnects. Fabrication is expected to be in liquid environment involving

buffer solutions, due to which there is a direct correlation between experimental and

fabrication conditions (variation in pH and temperature). Operation of these components is

expected to be in dry environment, and so the applicable modulation is temperature.

Synthetic short single-stranded DNA can be coupled to the substrate surfaces, based on self-

organization of the nucleic acid molecules, which is guided by the predefined

complementarity. This coupling reaction can be controlled by parameters such as

temperature, pH, and ionic concentrations.

A pH gradient enables discrete activation of hybridization zones, and is therefore a

novel application for microelectronic devices [18]. Buffering caused by histidine is vital to

13

Figure 2.5. (a) DEP forces v/s distance from the electrode surface in both 2D and 3D electrodes (b) Relationship between change in temperature and applied voltage. Source: Erickson, D., D. Li, and U. J. Krull. “Modelling of DNA Hybridization Kinetics for Spatially Resolved Biochips.” Analytical Biochemistry 317 (2003): 186-200.

maintain the pH as close to neutrality as possible to increase the rate and stringency of

hybridization of nucleic acid molecules. If the pH is lowered below a critical threshold value,

hybridization will be hindered. Therefore, in alleviating the detrimental effects of variation in

pH, caused by the hydrolysis reaction at the anode, a species beneficial to the hybridization

reaction is generated.

Current flowing through a conductor causes heating up of the device due to the

conversion of electrical energy into heat. This phenomenon is referred to as Joule heating and

is mathematically expressed as: Q = V * I * t. Thus joule heating is proportional to the

magnitude of voltage applied as well as the time duration, and this in turn determines the

degree of temperature variation [33].

Joule heating is induced by interactions between the electrons flowing through the

current, and the atomic ions that make up the body of the conductor. Charged particles in an

electric circuit get accelerated when exposed to an electric field. Some of these tend to lose

their kinetic energy, each time they collide with an ion. The increase in the kinetic or

vibrational energy of the ion manifests itself as heat and a corresponding rise in temperature

of the conductor. This illustrates the transfer of energy from the electrical power supply to

the conductor with which it is in thermal contact.

14

CHAPTER 3

DESIGN & MICROFABRICATION OF 3D

BIONANOELECTRONIC CHIP

In this chapter, we propose to develop a 3-dimensional architecture consisting of 3-

dimensional gold-coated micro-electrodes, separated by a gap of 15µm, which is equal to or

less than the length of λ-DNA. This will serve as the characteristic platform, and eventually

we arrive at an optimized design. The micro-fabrication procedure is based on negative

photolithography process using a negative photoresist, SU-8(10). The chemical structure of

SU-8 molecule is illustrated in Figure 3.1. [34]. The procedure begins with dicing a Silicon

wafer into 1cm x 1cm chips, and cleaning these thoroughly. The negative photoresist SU-

8(10) is then poured onto the chip followed by spin coating the chip. The chip is then

prebaked and allowed to cool down at room temperature. A mask containing the desired

feature is then properly aligned onto the chip, and exposed to U.V. light which polymerizes

the feature on regions where the photoresist is exposed. This is followed by post-baking the

chip, after which a layer of gold is sputtered onto the substrate. The chip is then developed

using SU-8 Developer which strips off the negative photoresist and the gold layer from

regions that did not receive U.V. light [35].

Figure 3.1. SU-8 molecule. Source: Davis, James and James Eson. “SU-8 Photoresist Processing.” In Microchem, 234-236. Lake George: Quality Science Labs, 2010.

15

The negative photoresist SU-8 was originally invented by IBM in 1989, but is now

sold by Microchem and Gersteltec. SU-8 resins consist of eight epoxy groups per molecule

due to which the polymer exhibits very high functionality. It is a very viscous polymer with

UV maximum absorption at 365nm wavelength. Solidification of the material occurs during

UV exposure when SU-8 molecular chains cross-link. SU-8 is highly transparent in the

ultraviolet region, allowing for processing of very thick film up to 2mm with nearly vertical

side walls [36, 37].

There are a few advantages of using SU-8 over Shipley in our research. First, SU-8 is

more efficient I patterning high aspect ratio >20, which enables the development of a 3D

structure with more width for the whole feature, and a smaller gap distance between the two

electrodes. Second, SU-8 exhibits better adhesion to the silicon substrate as well as to the

gold layer, as compared to Shipley’s positive photoresist. Third, after U.V. exposure and

stripping, the highly cross-linked structure of SU-8 gives it more resistance to chemicals and

to radiation damage [34]. Fourth, Su-8 also exhibits a higher temperature resistance, in

comparison to positive photoresists [38, 39].

3.1 CHIP DESIGN & MASK LAYOUT

This section describes the basic design and layout of the different masks used for

experimentation. The nomenclature for the various chip designs was inspired by Persian and

Indian mythology.1

3.1.1 Design I Mask

This mask design is a 2x1 microarray, consisting of over 2072 3D diamond-shaped

carbon-based electrodes. Each electrode has a diameter of around 75µm, and the spacing

between adjacent electrodes is around 150µm. A view of the mask layout and a portion of the

chip used for our experiment are shown in Figure 3.2.

1 Mithras: The ancient Persian God of light; Indra: King of Demi-gods or devas; Lord of heaven

16

Figure 3.2. Image of the mask layout (left); Chip used for experimentation (right).

3.1.2 Design II Mask (“Mithras” Feature)

This mask consists of many features of which the ‘Mithras’ design is of interest. This

design consists of only two electrode features separated by a gap of 10µm as shown in Figure

3.3. The layout consists of six 1cm×1cm regions which are populated on different parts of a

4inch (100mm) mask file built using CoventorWare®. The mask file is then sent out to be

printed, and it comes back as a transparent film which can be used for the microfabrication of

3-D chips.

Figure 3.3. Design II Mask Layout and Mithras feature design.

3.1.3 Design III Mask (“Indra” Feature)

This design is similar to the Mithras feature in that it also consists of only two

electrodes which are separated by a gap of 15µm as shown in Figure 3.4.

17

Figure 3.4. Design II Mask Layout and Indra feature design.

Table 3.1 describes the dimensions of the different mask designs used for

experimentation.

3.2 3-D NEGATIVE PHOTOLITHOGRAPHY PROTOCOL

This section describes the detailed negative photolithography process used for

microfabrocating the chips.

3.2.1 Wafer Preparation

The 3-D Biomicroelectronic architecture is fabricated using the facility at SDSU

MEMS Lab clean room (Class-100). The procedure starts with a clean non-oxidized silicon

wafer, with a diameter of 4 inch and 0.5 m thickness. The wafer is then diced into

1cm×1cm die chip. The chip is then thoroughly cleaned with acetone, Isopropyl alcohol

(IPA) and D.I. Water, and then blow-dried with a nitrogen gun. The chemical reagents used

for cleaning are sown in Figure 3.5.

3.2.2 Dehydration Bake

The chip is then dehydrated on an oven plate at 65° C for 60s to make sure that the

chip is completely dry. Then, it is kept out until it cools down to room temperature.

18

Table 3.1. Summary of the Chip Designs Used for Experimentation

Design Name Spacing Dimension (µm)

Image

Design I 150

Mithras 10

Indra 15

Figure 3.5. Clean room station.

19

3.2.3 Photoresist Coat

The chip is mounted on the spin coater (shown in Figure 3.6) and a puddle of SU-

8(10) is applied on to the chip carefully in a single dispense to prevent any air bubble

formation on the coating surface.

Figure 3.6. Spin coater.

Multiple drops may trap air bubbles which can decrease the quality of the features.

The chip is then spin-coated at a speed of 2000 rpm and gradually increased to 3000 rpm for

45 seconds, under a suction 10-9 Torr via a vacuum pump. By varying the viscosity, speed

and time parameters we can produce the coating thickness of 15 to 90 µm. The time and

speed rate were determined with respect the following spin curve and running several lab

experiments.

3.2.4 Soft Bake

After the resist has been applied to the substrate, the chip is soft baked at 65oC for 10

minutes as shown in Figure 3.7. The temperature is then increased from 65oC to 85oC

gradually for 10 minutes. The chip is then left on the oven at 95oC for an additional 15

minutes in order to evaporate the solvent and increase the density of the film. The soft

baking time depends on the solvent evaporation rate, which is influenced by the rate of heat

transfer and ventilation.

3.2.5 Expose

The mask is then cleaned and aligned on the chip, which is mounted on an OAI U.V. light

source as shown in Figure 3.8, suction is and suction is applied through a vacuum pump.

20

Figure 3.7. Hot plate.

Figure 3.8. OAI U.V. light source.

The U.V. exposure dose depends on film thickness and is ~6mW/cm2. If we assume the light

intensity of the UV source is ~15mW/second, the exposure time is calculating as follow:

Exposure time= exposure dose / measured intensity. Based on this equation and our lab

experiments the best exposure time is 30s. At this point, the mask aligner set up is slid and

exposed to the UV source.

21

3.2.6 Post-Bake

Following exposure, a post bake must be performed to selectively cross-link the

exposed portions of the film. According to our fabrication experiments, the backing

temperature starts with 65oC for 10 minutes; it is then increased gradually to 95oC for 20

minutes, and then to 120oC for 5 more minutes. The reason for this gradual ramping is SU-8

readily cross-linked and can result in a highly stressed film. The chip is then removed and

cooled down slowly at room temperature [40].

3.2.7 Gold Sputtering

An image of the gold sputtering machine used for experimentation is shown in Figure

3.9. The chip is loaded onto the stage and placed inside the bell jar. The vacuum pump is

turned on, and the chamber is repeatedly flushed with argon until the vacuum gauge reads

bellow 70 mTorr. The timer is set for 10 minutes and the high voltage is turned on. To start

sputtering, the voltage is set to 9V and care is taken to maintain the current below 10mA. At

the, the high voltage, main power, and the argon tank are turned off, and the sample is

removed from the chamber.

Figure 3.9. Gold sputtering machine.

22

3.2.8 Development/Stripping

300 ml SU8 developer solution is poured into the ultrasonic bath (shown in Figure

3.10), and the chip is left there for 5 min. It is then removed, rinsed with DI water for 10s and

blow dried with the nitrogen gun. At this point we are able to see the gold layer completely

developed on the feature with naked eyes.

Figure 3.10. Ultrasonic bath.

3.2.9 Imaging

Finally, the chip is viewed under an optical microscope to visualize the features. The

thicknesses of the feature can be measured using Keyence LT-9000M laser measurement

system which has a resolution of 0.01. Figure 3.11 illustrates the results of some of the chips

used for the experimentation.

23

Figure 3.11. Images of the various features used for experimentation.

24

CHAPTER 4

ELECTROCHEMISTRY CHARACTERIZATION

In this chapter, an exhaustive investigation to determine the degree of variation in pH

for the quantitative characterization of 3D electrodes on bionanoelectronics platform is

described. This chapter also explains the dependence of pH on time, spacing between the

electrodes, and variation of pH along the length of the electrodes. Subsequently, a finite

element analysis of the 3D gold electrodes is described to simulate the degree of variation of

pH with respect to an externally applied DC bias. Similar conditions were maintained, as

when the experiment is performed, in order to draw out a comparison between the simulation

results and the experimental results.

4.1 PH-BASED CHARACTERIZATION OF 3D METAL

ELECTRODES

A number of experiments have been performed to determine the degree of variation

of pH as a function of the potential difference applied. The experiments have also confirmed

the dependence pH on the spacing between the electrodes. An analysis of the variation of pH

at the anode with time has also been performed. In addition, the variation of pH along the

length of the electrodes and at the spacing w.r.t. a DC bias has also been carried out.

4.1.1 Description of the Equipment Used

This section includes a brief description of the equipment used for the measurement

of pH on the 3D gold sputtered micro-electrodes.

4.1.1.1 PH METER (JE671-T)

As shown in Figure 4.1, JE671T is a high performance laboratory bench instrument

used for the measurement of pH, mV and temperature. It has the following specifications:

Table 4.1 lists the following specifications:

25

Figure 4.1. Screen grab of JE671T pH meter.

Table 4.1. List of Specifications for JE671T pH Meter

SPECIFICATION VALUE

Range 00.00 to 14.00

Resolution 0.01

Accuracy +/- 0.1

4.1.1.2 REFERENCE ELECTRODE (DRI-REF

450)

The Dri-Ref 450 reference electrode (shown in Figure 4.2) exhibits a stable potential,

low electrode resistance, and very low electrolyte leakage. The electrode has a diameter of

450µm.

Figure 4.2. Images of Dri-Ref 450.

4.1.1.3 BEETRODE PH ELECTRODE

(NMPH2B)

The Beetrode pH electrode (shown in Figure 4.3) is a miniature, dry-coated pH wire

electrode with 100µm sensing tip, which makes it ideal for monitoring rapid pH changes in

very small locations. Due to its dry state chemistry, the Beetrode exhibits a larger Eo as

26

Figure 4.3. Images of Beetrode.

compared to conventional glass electrodes. It consists of a solid-state pH sensor with ideal

characteristics over a wide pH range, and requires a separate reference electrode for pH

measurements.

Table 4.2 lists the following specifications:

Table 4.2. List of Specifications for Beetrode

SPECIFICATION VALUE

Tip Diameter 100 µ (0.1mm)

Tip Length 2 mm

Response Time 1 sec (90%)

pH range 0 – 14

Slope Nernstain

Resistance 100 kΩ

4.1.1.4 Z-BEE-CAL

In order to obtain pH-scale readings on standard pH meters, a Z-BEE-CAL offset

device is used as shown in Figure 4.4. The Z-BEE-CAL is a small battery-operated

compensator that provides for the adjustment of the electrode offset potential, in the range of

0 to -450mV, to enable the Beetrode to produce standard pH-scale readings.

Figure 4.4. Image of the Z-BEE-CAL battery.

27

4.1.2 Calibration Process

Proper calibration of all the equipments used for experimentation is vital in order to

ensure accuracy of the data recorded. All the equipments were carefully calibrated, and the

calibration process has been explained in the following sections.

4.1.2.1 CALIBRATION OF PH METER

The device has to be dual point standardized in order to obtain accurate pH

measurements. A separate pH electrode has been provided to calibrate this instrument. 50mM

L-Histidine Buffer is prepared to be used as the sample for calibration purposes. The

calibration of the pH meter is performed as follows:

1. The pH electrode is immersed in the buffer solution whose pH is to be determined.

2. The TEMPERATURE control of the instrument is set to the temperature of the buffer solution.

3. The MODE switch is then turned to pH, and sufficient time is allowed for the pH electrode to reach the temperature equilibrium with the histidine buffer solution, and for the device to give an accurate reading of the solution.

4.1.2.2 CALIBRATION OF Z-BEE-CAL

The equipment is set-up, by connecting the Beetrode, Z-BEE-CAL battery, as shown

in Figure 4.5.

Figure 4.5. Experimental Beetrode set-up.

1. The tips of the Beetrode and the Reference electrode are immersed in a buffer solution with a pH of 7.

2. The MODE of the pH meter is then set to record pH, and the meter’s calibration knob is adjusted to the mid-position.

3. The offset control screw on the Z-BEE-CAL is then adjusted until the pH meter displays a reading of 7.0 pH.

28

4.1.2.3 CALIBRATION OF BEETRODE

1. The pH meter is set to the millivolt (mV) mode.

2. The tips of the Beetrode and the reference electrode are immersed in a buffer solution with a pH of 4.0. Sufficient time is given to obtain a stable pH reading, after which the pH meter measurement was recorded.

3. The above step is repeated with a buffer solution of pH 7.0.

4. The above step is again repeated with a buffer of pH 10.0.

5. The results are then plotted, with the mV readings on the Y-axis, and the pH readings on the X-axis.

Ideally, a linear Nernstian plot, as shown in Figure 4.6 [33]. should be obtained, and

the correlation should equal about 59.2mV/pH unit.

Figure 4.6. Ideal Nernstian plot. Source: Tay, F. E. H, L. Yu, A. J. Pang, and C. Lliescu. “Electrical and Thermal Characterization of a Dielectrophoretic Chip with 3D Electrodes for Cells Manipulation.” Electrochimica Acta 52, no. 8 (2007): 2862-2868.

Table 4.3 displays the readings obtained during the calibration process.

Table 4.3. Calibration Results

pH mV

4.03 164

5.36 75

6.81 0

9.85 -176

29

The plot for these values is shown in Figure 4.7. The slope of this plot was calculated

as follows:

Slope = . .

= 58.41 mV/pH unit

Figure 4.7. Calibration plot.

This value is close to the actual value, and thus the Beetrode was successfully

calibrated. The electrode calibration is to be checked routinely, before each experiment,

because of the baseline drift that occurs as the electrode ages. Baseline drift should be

maintained at a value less than 2.5mV.

4.1.3 Main Experimental Procedure

The experimental analysis for variation in pH was carried out in the following steps:

1. The electrode calibration was checked every time the experiment was repeated in order to make sure the pH meter displayed the correct readings for pH.

2. 50mM L-Histidine buffer, weighing 0.76g, was prepared and its ph was recorded.

3. The probes for applying the DC bias were then set up on the chip, along with the beetrode and the reference electrodes for pH measurement.

4. A drop of the freshly prepared histidine buffer was added so as to immerse only the tips of the beetrode and the reference electrode, without touching the probes.

5. DC bias was applied, starting with 1V.

6. The readings of pH at the anode and cathode were then recorded, as displayed by the pH meter.

164

75

0

-176-200

-150

-100

-50

0

50

100

150

200

4.03 5.36 6.81 9.85

mV

pH

Calibration of Beetrode

30

7. The bias was then increased to 2V and the corresponding pH readings at anode and cathode were recorded.

8. Finally, the bias was increased to 3V and the readings were noted down.

4.1.4 Experiment with Design I Chip

This section elaborates the experimental procedure followed for recording the

variation of pH with respect to an externally applied electric bias, as well as the data recorded

during the course of the experiment.

4.1.4.1 WIRE BONDING

The tips of both the reference electrode and Beetrode should be completely immersed

in solution for appropriate measurement of pH. For this purpose, insulated wires are bonded

onto the bump pads of the chip, and the insulation is peeled off from the ends of the wires.

This insulation prevents the voltage from flowing into the histidine solution, and makes sure

that the voltage is applied only at the traces of the chip.

Wires bonded onto the bump pads of the chip serve as probes through which the DC

bias can be applied at the traces of the chip. Wire bonding is performed as follows:

1. The insulation on the wires to be bonded is peeled off from the ends.

2. A 50:50 mixture of silver and golden epoxy is applied on the wires, held at the bump pads of the chip so as to increase the conductivity of the wires.

3. The chip is then heated on a hot plate at 85°C for 45 minutes.

4. A 50:50 mixture of glue is then applied so as to bond the wires onto the bump pads of the chip.

5. The chip is again heated on the hot plate at 85°C for 30 minutes.

4.1.4.2 MAIN EXPERIMENTAL SET-UP

The chip is then used to perform the quantitative characterization of variation in pH.

At the beginning of the experiment, the traces in the chip are singled out using a needle, so

that only two traces are used for performing the experiment as shown in Figure 4.8. A

positive bias is applied to one trace which functions as the anode, and a negative bias is

applied to the other trace which functions as the cathode. The procedure mentioned in

Section 5.1.3. is then followed.

The pH of a newly prepared 50mM L-Histidine buffer is recorded before starting the

experiment. A DC bias is then applied at the traces, and the Beetrode is moved from one

31

Figure 4.8. Main experimental set-up for Gen I Chip.

electrode to the next, first at the anode, and then at the cathode, and the corresponding pH

values at each electrode are recorded. An average of the pH values at the anode and the

cathode is then determined. The above procedure is carried out for a bias of 1V, 2V, and 3V,

with the biasing being slowly increased from 0V to 1V, 1V to 2V, and so on.

4.1.4.3 RESULTS & DISCUSSION

The experiment was conducted on a total of 7 chips, each with the same design and

micro-fabricated using the same mask layout. On an average, the following pH values were

observed: pH of 50mM L-Histidine Buffer = 6.76.

Table 4.4 summarizes the results obtained for pH variation in Design I chips.

It can be seen from Figure 4.9 that there is a continuous drop in pH at the anode up to

a magnitude of 0.15. On the other hand, there is a continuous rise in pH at the cathode, with

the net rise being 0.07. However, this variation in pH seems to be almost negligible, and so

we came up with a new design with a very small gap between the electrodes.

4.1.5 Experiment with Mithras

This section describes the experimentation procedure and results for Mithras.

32

Table 4.4. Experimental Results for Design I-pH Variation

DC Bias Applied Average pHAnode Average pHCathode

0 6.76 6.74

1 6.72 6.78

2 6.88 6.79

3 6.59 6.81

Figure 4.9. Variation of pH with respect to voltage for Design I.


The experimental procedure described in Section 4.1.3 is carried out. No wire

bonding is required for this design due to the absence of any traces and bump pads (since

there are only 2 electrodes), which means that the voltage bias is applied directly at the

electrode as shown in Figure 4.10.

6.74

6.696.4

5.97

6.74

6.78 6.79 6.81

5.4

5.6

5.8

6

6.2

6.4

6.6

6.8

7

0 1 2 3

pH

Voltage (V)

Average pHAnode

Average pHCathode

33

Figure 4.10. Main experimental set-up for Mithras.





Table 4.5 summarizes the experimental results for pH variation with Design II

(Mithras).

Table 4.5. Experimental Results for Design II-pH Variation (Mithras)


0 6.79 6.77

1 5.33 7.21

2 4.99 7.86

3 4.45 8.23

Again, it can be observed from Figure 4.11 that there is a continuous drop in pH at

the anode up to a magnitude of 2.34. At the same time, there is a continuous rise in pH at the

34

Figure 4.11. Variation of pH with respect to voltage for Mithras.

cathode, with the net rise being 1.46. Thus with the new design, and a much smaller spacing,

we were able to achieve a significant variation in pH.

4.1.6 Experiment with Indra

This section describes the experimentation procedure and results for Indra.


The experimental procedure described in Section 4.1.3 is carried out. No wire

bonding is required for this design due to the absence of any traces and bump pads (since

there are only 2 electrodes), which means that the voltage bias is applied directly at the

electrode. Figure 4.12 illustrates the experimental set-up for design 3 chips.





Table 4.6 summarizes the experimental results for pH variation with Design III

(Indra).

6.795.33 4.99

4.45

6.777.21

7.86 8.23

0

1

2

3

4

5

6

7

8

9

0 1 2 3

Voltage (V)

pH Anode

pH Cathode

35

Figure 4.12. Main experimental set-up for Indra.

Table 4.6. Experimental Results for Design III-pH Variation (Indra)


0 6.93 6.93

1 5.98 7.66

2 4.47 8.01

3 3.92 8.78

Again, it is confirmed from Figure 4.13 that there is a drop in pH at the anode up to a

magnitude of 2.06. At the same time, there is a continuous rise in pH at the cathode, with the

net rise being 1.12. Thus with the new design, and a much smaller spacing, we were able to

achieve a significant degree of variation in pH.

4.1.7 Discussion of Results

It can be seen from Figure 4.14 that the dimension of the gap between the anode and

the cathode is a significant factor in determining the degree of variation in pH. It can be seen

from the graph below that as the spacing between the electrodes decreases, there is a more

significant change in pH.

36

Figure 4.13. Variation of pH with respect to voltage for Indra.

Figure 4.14. Dependence of pH on spacing between the electrodes.

A number of chips were micro-fabricated for the pH characterization of 3D gold

electrodes on silicon substrate in order to gather a wide range of data points and ensure

accuracy of results. A rough estimate of this is shown in Figure 4.15.

4.2 EXPERIMENTAL ANALYSIS OF THE TEMPORAL

VARIATION OF PH

A number of experiments were carried out to observe the variation of pH with time

for a range of externally applied voltage. Figure 4.16 describes the temporal variation of pH.

6.935.98

4.473.92

6.937.66 8.01

8.78

0

1

2

3

4

5

6

7

8

9

10

0 1 2 3

Var

iati

on

of

pH

DC Bias

pH_Anode

pH_Cathode

0.15

2.06

2.34

0.07

1.12

1.46

0

0.5

1

1.5

2

2.5

150 15 6

pH

Var

iati

on

Electrode Spacing (µm)

Net Drop

Net Rise

37

Figure 4.15. Estimate of the total number of chips microfabricated for each design.

Figure 4.16. Temporal variation of pH with respect to voltage.

The experimental procedure described in section 4.1.3 was carried out. However,

when the DC bias was applied the changes in pH were recorded over a time period of 120

seconds.

Table 4.7 summarizes the experimental results for temporal variation of pH with

respect to an externally applied D.C. bias.

4.3 NUMERICAL MODELING OF 3D ELECTRODES FOR

PH CHARACTERIZATION

In this research, FEMLAB (COMSOL, 3.5a) multi-physics FEA modeling software is

used for performing this simulation. The mesh sizes differ depending on the geometry under

710

11 Design I

Mithras

Indira

0

2

4

6

8

0 30 60 90 120

pH Variation

Time (s)

pH_1V

pH_2V

pH_3V

38

Table 4.7. Experimental Results for Temporal Variation of pH

Time (s) pH_1V pH_2V pH_3V

0 6.93 6.91 6.94

30 6.72 6.52 6.26

60 6.30 5.97 5.21

90 6.09 5.80 4.80

120 6.04 5.71 4.52

consideration; however quadratic 2D and 3D elements are used with enough refinement for

convergence for 2D and 3D models, respectively. Regions near high convective and electro

migratory fluxes such as electrodes are meshed with finer elements.

This chapter describes a major coupling reaction that occurs between equations for

generation and migration of H+ and His+. The coupling between H+ and His+ species is strong

around the anodes, where H+ ions being generated are subsequently consumed by

zwitterionic histidine. The concentration of H+ ions at any given time is, therefore,

continuously being replenished, while undergoing transportation through diffusion and

electro-migration in addition to consumption by zwitterionic histidine. Therefore, due to the

strong coupling between these sets of equations, a nonlinear solution approach is used.

4.3.1 Model Geometry

The numerical modeling of the effects of protonation of histidine in electronically

active bionanoelectronics architecture requires consideration of a number of physical

phenomena, which are described by a series of partial differential equations and chemical

equilibrium reaction equations. To highlight this discussion, a model based on the Indra

feature developed for experimental analysis is considered as shown in Figure 4.17.

The model consists of two electrodes, one of which functions as the anode and the

other as the cathode. The electrodes are separated by a gap of 15µm and the dimensions of

each electrode are shown in Figure 4.18.

39

Figure 4.17. Illustration of the Bionanoelectronics model.

Figure 4.18. Electrode geometry.

At the anode, hydrolysis of water results in the generation of H+ ions, represented by

the following chemical reaction:

At the cathode, hydrolysis of water results in the generation of OH- ions as shown below:

The protonation of zwitterionic histidine results in the generation of protonated histidine ions

at the anode, given by the following chemical equilibrium reaction.

Note that the short-hands His+ and Hisz are used for representing protonated histidine and

zwitterionic histidine respectively.

The pH of the system is determined from the hydrogen ion concentration based on the

relationship, pH=−log [H+].

eOHHgasOOH 424)(4 222

)(222 22 gasHOHeOH

HisHHisHisd

Hisa

K

Kz

,

,

+ -

40

4.3.2 Description of the Physics Used

Table 4.8 summarizes all the boundry conditions used for numerical modeling and

simulation.

4.3.2.1 ELECTROSTATIC SYSTEM

The first physics deals with the distribution of potential and electric fields in the

bionanoelectronics architecture. It is described through laplacian equation for fields as

shown: σ2V = 0 where σ is the conductivity of the buffer and V is the electric potential

distribution. No external source of current, apart from biasing is assumed; hence the right

hand side of the equation is zero

4.3.2.2 GENERATION AND MIGRATION OF

H+ AND OH-

IONS

The number of H+ and OH- ions is given by Faraday’s Equation: n = I.t / zF

where n is the number of moles; I is the current, z is the number of electrons involved in the

reaction, and F is the Faraday’s constant which is equal to 96,500.

Further details of the parametric analysis have been displayed in Figures A.1, A.2,

A.3, A.4, A.5, A.6, A.7, and A.8 of Appendix A.

The migration of H+ and OH- ions is given by Nernst-Planck equation that accounts

for diffusion, convection and electro-migration and is given as:

where D – diffusion rate of H+ ion, CH+ is the concentration of H+ ions at a given time, z

– valency of H+ ions, R – reaction rate for producing the H+ ions, um,H+ –

electrophoretic mobility of H+ ions, u – velocity of fluid flow in the flow cell containing the

microarray, and t – time. The terms for OH- ions are similar and are obtained by replacing H+

with OH- in the above descriptions.

HHHHmHHH

H cuRVFcuzcDt

c)(

,

OHOHOHOHmOHOHOH

OH cuRVFcuzcDt

c)(

,

H

H

H

41

T

able

4.8

. Su

mm

ary

of t

he

Bou

nd

ary

Con

dit

ion

s U

sed

in t

he

Nu

mer

ical

Mod

el

Ph

ysic

s B

oun

dar

y C

ond

itio

ns

R (

Rea

ctio

n T

erm

s)

Con

stan

ts

Ele

ctro

stat

ics

@ A

nod

es

1 to

3V

@ C

ath

odes

-1 to

-3

V

----

----

-

(con

duc

tivity

) =

60

S/c

m

Gen

erat

ion

and

Mig

rati

on o

f H

+

ions

.

@ W

alls

Insu

late

d (z

ero

flux

)

@ E

lect

rode

s

Zer

o fl

ux a

t all

ele

ctro

des

=

0

@ A

nod

es

RH

+ =

((J*

Are

a)/9

6500

)/(V

olum

e))-

Ka,

His*c

H+*

(cH

isZ-

c His

+) –

Kd,

His

*cH

is+)

J –

curr

ent d

en

sity

The

sec

ond

term

rep

rese

nts

H+

cons

umpt

ion

by

His

z .

Eve

ryw

her

e E

lse

R H

+ =

0

u m, H

+ =

4x1

0-7 m

2/V

.s

z =

1

DH

+ =

9.3

x10

-9 m

2/s

(tab

le c

ontin

ues)

HH

Hm

HH

cu

VF

czu

cD

N,

42

Tab

le 4

.8. (

Con

tin

ued

)

Gen

erat

ion

and

Mig

rati

on o

f

His

+ io

ns.

@ W

alls

Insu

late

d (z

ero

flux

)

@ A

ll D

omai

n

At t

= 0

, con

stan

t CH

is =

50m

M

@ E

lect

rode

s

Zer

o fl

ux a

t all

ele

ctro

des

= 0

Eve

ryw

her

e

R H

is+

= K

a,H

is*c

H+*

(cH

isZ-

c His

+) –

Kd,

His *

c His

+)

u m,H

is+

= 1

0-13

m

2/V

.s

z =

1

D H

is+

= 2

.27

x10-8

m2/s

Ka,

His =

0.0

5

m3/m

oles

.sec

K

d,H

is =

0.0

005

/ sec

H

isH

ism

His

His

cu

VF

czu

cD

NH

is,

43

4.3.2.3 PROTONATION AND DE-PROTONATION OF ZWITTERIONIC

HISTIDINE AND MIGRATION OF HIS+ IONS

The migration of His+ ions is also governed by Nernst-Planck equation, given as:

where Ka – the association rate for His+, Kd,His – the dissociation rate for His+, D –

diffusion rate of His+ ion, CHis+, is the concentration of His+ ions at a given time, z –

valency of His+ ions, R – the reaction rate for producing the His+ ions, and um, His+ –

electrophoretic mobility of His+ ions.

4.3.3 Solution of Numerical Model

In this 2D model, the anode is biased with positive potential while the cathode is

biased with negative potential. The buffer solution is 50 mM L-Histidine with a conductivity

of 60µS/cm. The transient solutions are run for 120 seconds which is a typical time frame for

collection and hybridization in electronically active microarrays [1-13]. In this study, the

effect of convective transportation is neglected unless otherwise stated. The effect of

permeation layer on the transport and accumulation of ions is also neglected. The quantities

of interest in the models are the generation, transport and accumulation of H+, His+, OH- ions

and pH changes near the anode.

For solving this model, the electric potential (V), electric field (E), and current

densities (J) are determined using the Laplacian equation. In this case, the system is

considered to be electro-neutral, and so the Laplacian equation can be solved independent of

the other system equations. However, the transport and accumulation of ions tend to

continuously modify the conductivity of the system, due to which the Laplacian equation is

solved simultaneously with all system equations. Moreover, as the H+ ions are generated,

they are simultaneously consumed by the histidine buffer which further modifies the pH [20].

HisHisHisHismHisHisHisHis cuRVFcuzcDt

c)(

,

His

His

His

His

44

4.3.3.1 SURFACE CONCENTRATION OF H+

IONS

When a DC bias is applied, the H+ ions at the anode undergo two rapid and

simultaneous processes. In the first process, the H+ ions are available to react with

zwitterionic histidine (Hisz), which is uniformly distributed in the domain. In the second

process, the H+ ions are electrophoretically transported and accumulated at the cathodes.

These two processes continue until diffusion, electro-migration and protonation reach steady-

state equilibrium. Meanwhile, His+ ions (protonated histidine) generated in this rapid reaction

are in turn transported by electro-migration and diffusion to the cathodes.

It can be seen from Figure 4.19 that the concentration of H+ at the cathodes is orders

of magnitude higher than that on the anodes. This is due to the electro-migration of a

majority of unprotonated H+ ions from anodes to cathodes, which is caused by the rather

large electrophoretic mobility of H+ ions in the order of 4×10−7m2/V-s, and the presence of a

large electric field at the anode which drives electro-migration.

Figure 4.19. Distribution of H+ ions at the anode and cathode.

It can be seen from Figures 4.20 and 4.21 that there is a greater concentration of H+

ions away from the spacing in case of the anode. On the other hand, for the cathode, the

concentration of H+ ions decreases with increasing distance from the spacing.

Figure 4.20. Temporal Variation of H+ ion concentration at 2 distinct points of the anode.

45

Figure 4.21. Temporal Variation of H+ ion concentration at 2 distinct points of cathode.

4.3.3.2 SURFACE CONCENTRATION OF HIS+

IONS

Figure 4.22 illustrates the distribution of histidine ions at the anode and cathode.

Figure 4.22. Distribution of His+ ions at the anode and cathode.

4.3.3.3 SURFACE CONCENTRATION OF HISZ

It can be seen from figures 4.23, 4.24, 4.25, and 4.26 that the consumption of

zwitterionic histidine is relatively low as compared to its initial concentration of 50mols/m3.

Also, since Hisz is not charged, the mode of transportation of these molecules is by diffusion.

Figure 4.23. Generation of His+ ions at anode.

46

Figure 4.24. Generation of His+ ions at cathode.

Figure 4.25. Distribution of zwitterionic Histidine along the anode and cathode.

Figure 4.26. Reduction of Hisz ions at anode.

4.3.4 Results & Discussion

Figure 4.27 summarizes the temporal variation of pH at the anode, for a range of

externally applied voltage.

It can be seen that the effect of histidine buffering on pH is minimal since the amount

of H+ ions that remain on the anode is reduced by electro-migration, as a result of the biasing

pattern that allows unobstructed electro-migration of H+ ions to the cathode.

47

Figure 4.27. Temporal variation of pH with respect to Electric Potential.

Using this FEA software, the maximum surface concentrations of H+ ions at the

anode were determined for DC bias of 1V, 2V, and 3V; and the corresponding pH values

were then calculated using the equation, pH=−log [H+].

Table 4.9 summarizes the simulation results obtained for pH variation in Design II

chips.

Table 4.9. Simulation Results for Design II- pH Variation (Cathode)

DC Bias (V) Max. H+ Concentration (mol/m3) pH = -log[H+]

1 2 X 10-6

5.7

2 9 X 10-5

4.05

3 3.5 X 10-4

3.5

Similarly, an analysis of the variation in pOH at the cathode was performed as

illustrated in Figure 4.28.

Using the COMSOL Multiphysics software, the concentrations of H+ ions at the

cathode were determined for 1V, 2V, and 3V. As already known, [H+][OH-] = 10-14, the OH-

48

Figure 4.28. Temporal variation of pH at the cathode.

ion concentration can be determined for each set of voltage bias. pOH can then be calculated

using the equation, pOH=−log [OH-]. Table 4.10 summarizes the simulation results obtained

for pH variation in Design III chips.

Table 4.10. Simulation Results for Design III-Results

DC Bias (V) H+ Concentration

(mol/m3)

OH- Concentration

(mol/m3)

pOH = -log[OH-]

1 3 X 10-7 3.16 X 10-8 7.5

2 1X 10-6 9 X 10-9 8.05

3 6.3 X 10-6 1.6 X 10-9 8.8

4.4 COMPARISON OF RESULTS

A comparison of the experimental and simulation results is shown in Figure 4.29.

It can be seen that there is a close correlation between the experimental and

simulation results for the degree of variation in pH at the anode and cathode of the 3D gold

electrodes for the proposed bionanoelectronic architecture.

49

Figure 4.29. Comparison of the experimental and simulation results for the degree of variation in pH.

0

0.5

1

1.5

2

2.5

Simulation Experiment

2.22.12

1.3

1.07ΔpH ΔpH_Anode

ΔpH_Cathode

50

CHAPTER 5

TEMPERATURE CHARACTERIZATION

In this chapter, an analysis of the degree of variation in temperature, as a consequence

of joule heating of the electrodes, for the quantitative characterization of 3D electrodes on

bionanoelectronics platform is described.

5.1 TEMPERATURE-BASED CHARACTERIZATION OF 3D

METAL ELECTRODES

The procedure followed for analyzing variation in temperature is outlined below:

1. 50mM L-Histidine buffer, weighing 0.76g, was prepared.

2. The control and test chips were set up on the stage of the 4-probe microscope.

3. The thermocouple (T1) was placed on the control chip, thermocouple (T2) was placed on the test chip, and probes for applying the DC bias were set up on the test chip.

4. A drop of histidine buffer was then added so as to immerse only the tips of both thermocouples, without touching the probes on the test chip.

5. A DC bias of 1V was applied on the test chip.

6. Temperature readings from both the thermocouples were recorded, as displayed by the thermocouple meter.

7. The bias was then increased to 2V and then to 3V, and each time, the corresponding readings of temperature on both the chips were recorded.

5.1.1 Experiment with Design I Chip

This section describes the experimentation procedure and results for Design I chip.


As shown in Figure 5.1, two chips based on the same design parameters are used to

perform the quantitative characterization of variation in temperature. One chip serves as the

Scientific Control to minimize the influence of variables like environment changes in the

immediate surroundings. The other chip represents the test chip, on which the voltage bias is

applied. At the beginning of the experiment, the traces in the chip are singled out using a

needle, so that only two traces are used for performing the experiment. A positive bias is

51

Figure 5.1. Main experimental set-up for Gen I Chip.

applied to one trace which functions as the anode, and a negative bias is applied to the other

trace which functions as the cathode. The procedure mentioned in Section 6.2 is then

followed.


The experiment was conducted on a total of 11chips, each with the same design and

micro-fabricated using the same mask layout. On an average, the following readings were

recorded:

Table 5.1 summarizes the experimental results obtained for temperature variation in

Design I chips.

It can be seen from Figure 5.2 that there is a continuous rise in temperature at the

anode and the cathode with increase in voltage, with a maximum rise of 1.2°C at the anode.

However, this variation in temperature seems to be insignificant, and so we repeated the

experiment with the new mask designs.

52

Table 5.1. Experimental Results for Design I-Temperature

DC Bias Applied Average TControl Average TAnode Average TCathode

0 21.3 21.3 21.4

1 21.4 21.7 21.8

2 21.3 22.1 22.0

3 21.3 22.5 22.2

Figure 5.2. Variation of temperature with respect to voltage.

5.1.2 Experiment with Mithras

This section describes the experimentation procedure and results for Mithras.


The experimental procedure described in Section 6.2 is carried out and the set-up is

shown in Figure 5.3. No wire bonding is required for this design due to the absence of any

traces and bump pads (since there are only 2 electrodes), which means that the voltage bias is

21.3

21.7

22.1

22.5

21.4

21.822

22.2

20.6

20.8

21

21.2

21.4

21.6

21.8

22

22.2

22.4

22.6

0 1 2 3

Temperature (°C)

Voltage (V)

Average T(Anode)

Average T(Cathode)

53

Figure 5.3. Main Experimental set-upapplied directly at the electrode. Moreover, the thermocouple is placed directly at the spacing between the electrodes for the subsequent experiments.



micro-fabricated using the same mask layout. On an average, the following readings were

recorded:


Design II chips.

It can be observed from Figure 5.4 that the degree of variation in temperature of the

test chip with respect to the control chip is 4.3°C. Thus with the new design, and a much

smaller spacing of 6µm, we were able to observe a significant variation.

5.1.3 Experiment with Indra

This section describes the experimentation procedure and results for Indra.

54

Table 5.2. Experimental Results for Design II-Temperature

DC Bias Applied TControl TSpacing

0 22.3 22.8

1 22.3 23.8

2 22.3 25.2

3 22.4 27.1

Figure 5.4. Grabs of temperature readings recorded on the Thermocouple meter.


The experimental procedure described in Section 7.2 is carried out and the set-up is

shown in Figure 5.5. No wire bonding is required for this design due to the absence of any

traces and bump pads (since there are only 2 electrodes), which means that the voltage bias is

applied directly at the electrode. Again, the temperature was recorded by placing the

thermocouple at the spacing between the electrodes for both the Control as well as the test

chips.



micro-fabricated using the same mask layout. On an average, the following values were

recorded:


Design III chips.

55

Figure 5.5. Main Experimental set-up.

Table 5.3. Experimental Results for Design III-Temperature

DC Bias Applied TControl TSpacing

0 21.7 22.1

1 21.7 23.1

2 21.7 25.2

3 21.7 26.7

Again, it is confirmed from Figure 5.6 hat the temperature continues to rise with

increase in the magnitude of potential difference across the electrodes. The degree of

variation in temperature of the test chip with respect to that of the control chip is 4.6°C.

A number of chips were micro-fabricated for the thermal characterization of 3D gold

electrodes on silicon substrate in order to gather a wide range of data points and ensure

accuracy of results as shown in Figure 5.7.

Similar conditions were maintained, as when the experiment is performed, in order to

draw out a comparison between the simulation results and the experimental results.

56

Figure 5.6. Screen grabs of temperature readings recorded on the Thermocouple meter.

Figure 5.7. Estimate of the total number of chips microfabricated for each design.

5.2 NUMERICAL MODELING OF 3D ELECTRODES FOR

TEMPERATURE CHARACTERIZATION

In this chapter, a finite element analysis of the 3D gold electrodes is described to

simulate the degree of variation in temperature with respect to an externally applied DC bias.

Similar conditions were maintained, as when the experiment is performed, in order to draw

out a comparison between the simulation results and the experimental results.

The 3D metal electrodes get heated when a DC bias is applied across them due to the

electrical resistance of the material. This phenomenon is termed as Joule heating, and causes

a variation in temperature.

5.2.1 Description of the Physics Used

This section describes the physics used for numerical simulation of pH and

temperature.

118

6Design I

Mithras

Indira

57

5.2.1.1 ELECTROSTATIC SYSTEM

The first physics deals with the distribution of potential and electric fields in the

bionanoelectronics architecture. It is described through laplacian equation for fields as

shown: σ2V = 0 where σ is the conductivity of the buffer and V is the electric potential

distribution. No external source of current, apart from biasing is assumed; hence the right

hand side of the equation is zero.

5.2.1.2 GENERAL HEAT TRANSFER

This physics deals with the phenomenon of Joule heating, according to the following

equation:

Where Q is joule heating, ρ is the resistivity of the material, α is the

Figures B.1, B.2, B.3, and B.4 of Appendix B illustrate the detailed parametric

analysis performed for this simulation.

5.2.2. Solution of Numerical Model

This section describes the numerical simulation results including surface temperature,

resistive heating and electric field distribution.

5.2.2.1 SURFACE TEMPERATURE

Figure 5.8 illustrates the surface temperature distribution along the anode and

cathode.

5.2.2.2 DEPENDENCE OF SURFACE

TEMPERATURE DISTRIBUTION ON

THERMAL CONDUCTIVITY

While solving the numerical model for temperature distribution, the thermal

conductivity of histidine buffer solution was varied, and the corresponding surface

temperatures were recorded and are shown in Table 5.4. It was found that as the thermal

conductivity increases, there is a drop in the surface temperature. Figure 5.9 displays the

graphical results.

58

Figure 5.8. Surface temperature along the anode and cathode; zoomed-in view of the temperature distribution at the spacing.

As a result of joule heating and increase in the applied voltage, the surface

temperature of the chip continues to increase, and there is a corresponding decrease in

thermal conductivity, due to the inverse-relation observed between these two parameters for

this particular design.

5.2.2.3 RESISTIVE HEATING

Figure 5.10 describes the resistive heating in between the electrodes.

5.2.2.4 ELECTRIC FIELD DISTRIBUTION

Electric field distribution can be seen clearly in Figure 5.11.

5.2.3 Results & Discussion

Figure 5.12 summarizes the temporal variation of temperature for a range of

externally applied voltage.

Using this FEA software, the surface temperature was determined for DC bias of 1V,

2V, and 3V and recorded as follows:

Table 5.5 summarizes the simulation results obtained for temperature variation in

Design III chips.

59

Table 5.4. Summary of the Variation of Surface Temperature with Thermal

Thermal

Conductivity

(W/m.K)

Surface

Temperature (K)

Model Image

0.00001 2152.2

0.0001 577.2

0.0005 358.2

0.001 329.2

0.005 305.4

0.01 302.4

0.05 300.1

0.1 299.8

60

Figure 5.9. Variation of temperature with thermal conductivity.

Figure 5.10. Resistive heating; zoomed-in view of the resistive heating at the spacing.

61

Figure 5.11. Electric Field; zoomed-in view of the electric field at the spacing.

Figure 5.12. Temporal variation of temperature with respect to voltage.

62

Table 5.5. Simulation Results for Design III-Temperature

DC Bias (V) Surface Temperature (K) ΔT

1 294.62 0.62

2 296.46 2.46

3 299.57 5.54

5.2.4 Comparison of Results

A comparison of the experimental and simulation results is shown in Figure 5.13.

Figure 5.13. Comparison of the experimental and simulation results for the degree of variation in temperature.

It can be seen that there is a close correlation between the experimental and

simulation results for the degree of variation in temperature of the 3D gold electrodes for the

proposed bionanoelectronic architecture.

Series10

2

4

6

Simulation Experiment

ΔT

Simulation

Experiment

63

CHAPTER 6

CONCLUSION

6.1 FUTURE RESEACH GOALS

The chapter highlights the prospective research that can be undertaken in the field of

bionanoelectronics.

This study investigates, through experimentation and numerical modeling, the degree

of variation in pH and temperature for characterization of 3D gold electrodes on

bionanoelectronics architecture. The 3D model framework developed consists of a number of

physical phenomena and chemical equilibrium reactions within an environment of

continuous generation of H+ ions and their subsequent consumption by histidine buffer, as

well as joule heating of the metal electrodes. The outcomes of this research can be

summarized as below:

1. The spacing between adjacent electrodes on a microarray is an important factor that influences the degree of variation in pH. It can be concluded from a range of experimental data that the greater the dimension of spacing, lesser is the variation in pH with respect to an externally applied DC bias.

2. pH measurements in electronically active microarrays are reported to have been measured a few microns above anodes to avoid interference with the target nucleotide accumulation. Thus, there is no reported pH measurement directly at the anodes. However, as shown by this research, there is sufficient data to demonstrate the pH measurements directly at the anode and an increase in basicity at the cathode. In addition, the ability to predict pH drops anywhere in the microarrays is a strong advantage offered by the numerical model reported here.

3. For the proposed bionanoelectronic architecture consisting of 3D gold electrodes based on the Indra feature, the simulation and experimental results were in close correspondence with each other. It can be concluded that a relatively stable pH environment can be maintained for the operation of DNA wires on gold-electrode based silicon platform. Moreover, the continuous generation of H+ ions is controlled by their subsequent consumption by the histidine buffer.

4. An analysis of the temporal variation of pH suggests that there is a continuous drop in pH at the anode with increase in the magnitude of externally applied voltage bias.

5. The research demonstrates the phenomenon of Joule heating to further characterize the 3D gold electrodes for the proposed bionanoelectronic architecture. For the degree

64

of variation in temperature, the simulation analysis supports the experimental results suggesting a significant degree of joule heating for the 3D gold micro-electrodes.

6. The thesis introduces for the first time in literature, data points for the micron level measurements of pH and temperature, which are further supported by FEMLAB simulation of the same.

7. Numerical modeling analysis of the degree of DNA hybridization for the proposed bionanoelectronic architecture suggests that the design enables relatively high degree of hybridization of single-stranded DNA at a spacing of 15µm between the 3D gold electrodes. Also, the pH window is sufficient to enable efficient hybridization of DNA for this architecture.

6.2 FUTURE RESEARCH

After successfully presenting the results in this research, a better understanding of the

pH and temperature sensitivity of 3D gold electrodes, and their influence on DNA

hybridization for an efficient bionanoelectronics architecture has been achieved. Going a step

further, investigation of other parameters in characterizing gold-based electrodes, and their

effect on DNA hybridization would greatly contribute towards this emerging field of

bionanoelectronics. Further research can be pursued in the following areas:

1. Effect of different buffers on the variation of pH for the all designs used in the research.

2. Mechanical characterization of 3D gold electrodes versus 3D graphite electrodes.

3. Experimental analysis and numerical modeling of the pH and temperature characterization with a DNA strand attached between the 3D gold electrodes.

Appendices C and D highlight some of the probable experimental investigations that can

be carried forward with respect to DNA hybridization. A summary of all the boundary

conditions which can be used for performing the numerical simulation have been listed in

Table C.1. The numerical simulation modeling results have been shown in Figures C.1 and

C.2. Based on the proposed architecture, the parametric analysis screenshots have been

shown in Figures D.1, D.2, D.3, and D.4.

65

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68

APPENDIX A

PARAMETRIC ANALYSIS FOR MODELING

VARIATIONS IN PH

69

Figure A.1. Subdomain settings-conductive media DC for pH.

Figure A.2. Boundary settings-conductive media DC for pH.

70

Figure A.3. Subdomain settings-electrokinetic flow (H+).

Figure A.4. Boundary settings-electrokinetic flow (H+).

71

Figure A.5. Subdomain settings-electrokinetic flow (His+).

Figure A.6. Boundary settings-electrokinetic flow (His+).

72

Figure A.7. Subdomain settings-electrokinetic flow (HisZ).

Figure A.8. Boundary settings-electrokinetic flow (HisZ).

73

APPENDIX B


VARIATIONS IN TEMPERATURE

74

Figure B.1. Subdomain settings-conductive media dc for temperature.

Figure B.2. Boundary settings-conductive media dc for temperature.

75

Figure B.3. Subdomain settings - general heat transfer.

Figure B.4. Boundary settings - general heat transfer.

76

APPENDIX C

NUMERICAL MODELING OF DNA

HYBRIDIZATION

77

DESCRIPTION OF THE PHYSICS USED

According to a research performed by a former colleague, Bhuvnesh Arya, the

hybridization of single stranded DNA molecules is governed by a chemical equilibrium

reaction equation, and the rate of this hybridization is governed by the rate law according to

which the rate of hybridization is a function of the concentration of all the species present in

the overall chemical reaction at a given time.

Target DNA molecule from the sample may either hybridize with the immobilized

DNA directly or may first be adsorbed onto the solid surface followed by diffusion over the

surface and hybridization. Considering direct DNA hybridization only, the DNA

heterogeneous hybridization reaction can be described by the following chemical reaction:

where CDNA,Probes represents ssDNA molecules immobilized on the solid surface that are

available for hybridization. According to this equation, target DNA molecules in the sample

(represented by CDNA) bind specifically to the DNA capture probes and form hybridized

double-stranded DNA molecules (whose concentration is represented by CDNA, Hybridized)

[29,30].

The transient first-order heterogeneous hybridization reaction rate equation that

governs the concentration of hybridized DNA molecules at any given time is given as:

where Ka,DNA is the forward reaction rate constant which governs the hybridization reaction

rate and Kd,DNA is the reverse reaction rate constant that determines the disassociation reaction

rate. Note that the term CDNA,Probes represents the difference between CDNA,Initial and

CDNA,Hybridized (i.e., CDNA,Probes = CDNA,Initial - CDNA,Hybridized). Further, the term CDNA,Initial is the

initial concentration of the capture probes before hybridization.

A diffusion only model is required to keep track of the hybridized double-stranded

DNA that accumulates on the anodes.

HybridizedDNAK

K

DNAobesDNA cccDNAd

DNAa

,Pr, ,

,

HybridizedDNADNAdHybridizedDNAInitialDNADNADNAa

HybridizedDNA cKcccKt

c,,,,,

, )(

DNAHybridizedDNA RcDt

cHybridizedDNA

HybridizedDNA

)(

,

,

,

78

where DDNA,Hybridized is the diffusion constant for DNA and RDNA represents the reaction rate

producing the hybridized double-stranded DNA.

SOLUTION OF THE NUMERICAL MODEL

The coupling between the equations for transport of ssDNA molecules and the

hybridized dsDNA is a mathematical necessity required to keep track of the hybridized

dsDNA that accumulates on the anodes. This coupling allows decrease in the concentration

of ssDNA molecules as they react with the capture probes on the anodes and get hybridized

to form dsDNA molecules. Due to this strong coupling between these sets of equations, a

nonlinear solution approach is used.

In the model, the electric potential (V), the electric field (E) and current densities (J)

are first determined by solving the Laplace equation. Subsequently, the equations governing

the generation and migration of H+ and His+ ions are solved simultaneously along with the

DNA hybridization since all these equations are highly coupled. The reason for the

simultaneous solution of these equations is that as H+ ions are being generated, they are

consumed by histidine which in turn modifies the pH in the buffer. This pH change will in

turn affect the hybridization process allowing actual DNA hybridization to take place only

through a narrow pH window.

It can be seen that the maximum surface concentration of hybridized DNA is closer to

the spacing at the anode.

79

Tab

le C

.1. S

um

mar

y of

th

e B

oun

dar

y C

ond

itio

ns

Use

d in

th

e N

um

eric

al M

odel

Phy

sics

B

ound

ary

Con

diti

ons

R (

Rea

ctio

n T

erm

s)

Con

stan

ts

Mig

rati

on o

f

DN

A

@ W

alls

Insu

lati

on (

zero

flu

x)

@ A

ll D

omai

n

At t

=0,

CD

NA =

50n

M

@ A

nod

e

Inw

ard

flux

(N

) =

)(

,P

r,

,

,,

Hyb

ridi

zed

DN

Aob

esD

NA

DN

AD

NA

a

Hyb

ridi

zed

DN

AD

NA

b

cc

cK

cK

(Thi

s co

uple

s th

e m

igra

tion

and

hybr

idiz

atio

n eq

uatio

ns)

----

----

- u m

= 1

.5x1

0-13

m2 /V

.s [

20]

z =

-1

D D

NA =

6.8

e-11

m2 /s

[20

]

Ka,

DN

A =

18 m

3 /

mol

es.s

ec

Kd,

DN

A =

6x1

0-5 /

sec

Hyb

ridi

zati

on

of D

NA

@ W

alls

Insu

late

d (z

ero

flux

)

@ A

nod

es

Hyb

ridi

zed

DN

AD

NA

b

Hyb

ridi

zed

DN

Aob

esD

NA

DN

AD

NA

aD

NA

cK

cc

cK

R

,,

,P

r,

,)

(

Eve

ryw

her

e el

se

R =

0

Ka,

DN

A =

18

m3

/

mol

es.s

ec [

20]

Kd,

DN

A =

6x1

0-5 /

sec

(CD

NA

, Ini

tial

) =

50x1

0-6 m

oles

/m3

(CD

NA

,Pro

bes)

=

1.3x

10-2

mol

es/m

3

80

Figure C.1. DNA Hybridization after 60s.

Figure C.2. Surface concentration of hybridized dsDNA.

81

APPENDIX D


HYBRIDIZATION OF DNA ON PROPOSED

ARCHITECTURE

82

Figure D.1. Subdomain settings-electrokinetic flow(ssDNA).

Figure D.2. Boundary settings-electrokinetic flow(ssDNA).

83

Figure D.3. Subdomain settings-diffusion (HybDNA).

Figure D.4. Boundary settings-diffusion (HybDNA).

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