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DEVELOPMENT AND FABRICATION OF ION-

SENSITIVE FIELD EFFECT TRANSISTOR (ISFET) FOR PH DETECTION, DNA IMMOBILIZATION AND

HYBRIDIZATION

CHONG SOON WENG

UNIVERSITI MALAYSIA PERLIS 2013

   

   

   

   

   

 

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Development and Fabrication of Ion-Sensitive Field Effect Transistor (ISFET) for pH Detection, DNA

Immobilization and Hybridization

By

Chong Soon Weng 1031710564

A thesis submitted in fulfillment of the requirement for the degree of Master of Science (Nanoelectronics Engineering)

School of Nanoelectronics Engineering UNIVERSITI MALAYSIA PERLIS

2013

   

   

   

   

   

 

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iii

UNIVERSITI MALAYSIA PERLIS DECLARATION OF THESIS

Author’s full name : Chong Soon Weng Date of birth : 27 August 1986

Title : Development and Fabrication of Ion-Selective Field- Effect Transistor (ISFET) for pH Detection, DNA Immobilization and Hybridization

Academic Session : 2012/2013

I hereby declare that this thesis becomes the property of Universiti Malaysia Perlis (UniMAP) and to be placed at the library of UniMAP. This thesis is classified as :

CONFIDENTIAL (Contains confidential information under the Official Secret Act 1972)

RESTRICTED (Contains restricted information as specified by the organization where research was done)

OPEN ACCESS I agree that my thesis is to be made immediately available as hard copy or on-line open access (full text) I, the author, give permission to the UniMAP to reproduce this thesis in whole or in part for the purpose of research or academic exchange only(except during a period of years, if so requested above).

Certified by:

SIGNATURE SIGNATURE OF SUPERVISOR

(NEW IC NO. / PASSPORT NO.) NAME OF SUPERVISOR

Date : Date :

   

   

   

   

   

 

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iv

ACKNOWLEDGEMENTS

First of all, I would like to express my heartfelt gratitude to Universiti Malaysia Perlis (UniMAP) and specifically Institute of Nanoelectronics Engineering (INEE) for providing the great facilities, machines, and materials to carry out my project scope of work.

Special thanks to my present main supervisor Professor Dr. Uda Hashim from whom I have learned a lot of technical skill and guidance in this project. I want to thank my previous main supervisor Cik Nur Hamidah Abdul Halim and my sub-supervisor Dr.

Nazree Derman for all the guidance and advices at times of need.

I also thank Encik Ramzan, Mira, Hasrul, Encik Hafiz b. Abd Razak and Encik Bahari Man who were a big help throughout my project. I am also very grateful to the financial support by MyMaster (Mybrains15) scholarship, Geran MOASciencefund, FRGS to purchase the machines and materials needed for this research.

Last but not least, thanks to my beloved family members, good friend Low Foo Wah, my all Nano Biochip Group fellows, Shahidah Arina Shamsuddin, Nazwa Binti Taib, Foo Kai Loong, Emi, Siti Fatimah, Khashif Farooq and Nizah, who shared a lot of knowledge, experiment findings and experience throughout the project.

 

   

   

   

   

   

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v

TABLE OF CONTENTS

PAGE

THESIS DECLARATION iii

ACKNOWLEDGEMENT iv

TABLE OF CONTENTS v

LIST OF TABLES ix

LIST OF FIGURES x

LIST OF ABBREVATIONS xiii

LIST OF SYMBOLS xvii

ABSTRAK xviii

ABSTRACT xix

CHAPTER 1 BACKGROUND 1

1.1 Introduction 1

1.2 Problem Statement 2

1.3 Research Objectives 3

1.4 Research Scopes 4

1.5 Thesis Organization 5

CHAPTER 2 LITERATURE REVIEW 6

2.1 Introduction 6

2.2 Metal Oxide Semiconductor Field-Effect Transistor (MOSFET) 6  

   

   

   

   

   

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vi

2.2.1 The Structure of an MOSFET 6

2.2.2 The Operating Principle of the MOSFET 7

2.3 Ion Sensitive Field-Effect Transistor (ISFET) 8

2.3.1 The Structure of an ISFET 8

2.3.2 The Operating Principle of the ISFET 9

2.3.3 Gate Materials 12

2.3.4 Silicon Nitride Properties 13

2.3.5 ISFET Device Encapsulation 19

2.3.6 Reference Electrode 20

2.3.7 Self Aligned Transistor Fabrication Method 21

2.3.8 Applications of ISFETs 22

2.4 Biologically Modified Field-Effect Transistor (BioFET) 24

2.4.1 DNA-FET 25

2.4.2 DNA Structure and Function 27

2.5 DNA Immobilization and Hybridization Detection 28

CHAPTER 3 METHODOLOGY 35

3.1 Introduction 35

3.2 Flowchart for ISFET Structure Fabrication 36

3.3 Wafer Preparation 36

3.4 Mask Design 37

3.5 ISFET Device Structure Fabrication 40

3.6 Morphological Characterization 45

   

   

   

   

   

 

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vii

3.7 Electrical Characterization with pH Buffers 45

3.8 ISFET Gate Surface Modification and DNA Immobilization and Hybridization

46

CHAPTER 4 RESULTS AND DISCUSSION 48

4.1 Introduction 48

4.2 Sheet Resistance Measurement 48

4.3 Oxide Thickness Measurement 49

4.4 ISFET Morphological Characterization 52

4.4.1 Energy Dispersive X-Ray Spectroscopy (EDAX) Results 52

4.4.2 X-Ray Diffractometer (XRD) Results 53

4.4.3 High Power Microscope (HPM) Results 54

4.4.4 Atomic Force Microscope (AFM) Results 62

4.5 Device Electrical Characterization 64

4.5.1 Preparation of ISFET for pH Testing 64

4.5.2 Wafer Dicing Results 64

4.5.3 Mounting and Wire Bonding Results 65

4.5.4 Encapsulation Results 66

4.5.5 Equipments Setup for Electrical Characterization 67

4.6 ISFET Device for pH Testing 67

4.7 ISFET Device Testing for Phosphate Buffer Solution (PBS) 70

4.8 pH Sensitivity of ISFET 73

4.9 ISFET for DNA Immobilization and Hybridization 75

   

   

   

   

   

 

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viii

4.10 Effect of DNA Complementary Concentration on ISFET Detection 77

CHAPTER 5 CONCLUSION 80

5.1 Introduction 80

5.2 Conclusion 80

5.3 Recommendation of Future Works 82

REFERENCES 84

APPENDICES 90

LIST OF CONFERENCE PROCEEDING 94

LIST OF ACHIEVEMENTS 95

   

   

   

   

   

 

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ix

LIST OF TABLES

NUMBER PAGE

Table 2.1 Engineering Properties of Silicon Nitride 17

Table 4.1 Sheet Resistance Measurements 51

Table 4.2 Before Dry Oxidation Process Measurements 52

Table 4.3 After Dry Oxidation Process Measurements 53

Table 4.4 Result showing three spot tested with EDX 54

Table 4.5 The volume percentages of PBS in DI water used in ISFET testing 63 Table 4.6 Measured 𝑉𝑡𝑕and sensitivity of ISFET in four pH buffer solutions 66 Table 4.7 Drain current at different DNA target concentrations 71  

   

   

   

   

   

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x

LIST OF FIGURES

NUMBER PAGE

2.1 Basic structure of an MOSFET 7

2.2 Device structure of an ISFET 9

2.3 𝐼𝐷/𝑉𝐷𝑆 curves of an ISFET with 𝑉𝑔𝑠 (a) and pH (b) as parameter (Bergveld, 2003).

11

2.4 Tetrahedral arrangement of nitrogen atoms 14

2.5 Arrangement of silicon with respect to nitrogen atoms 15 2.6 Schematic structure of a DNA-FET (GenFET) and the principle of

DNA-hybridisation detection (Schöning & Poghossian, 2002).

26

2.7 Schematic structure of double-strand DNA (Watson & Crick, 1953) 27 2.8 Immobilization of capture agent on silicon nitride surface (Wu, et

al., 2006).

30

2.9 Entire attachment process on Si(100) surfaces (Lin, et al., 2002). 31 2.10 Potentiometric detection of various DNA recognition events using

genetic FETs (T Sakata & Miyahara, 2006).

33

2.11 Scheme for DNA sequencing based on primer extension using genetic FET. DNA polymerase assisted repeatedly the incorporation of deoxynucleotides at the gate (T Sakata & Miyahara, 2006).

34

3.1 The flow of the research 35

3.2 Fabrication process for ISFET device structure. 36

3.3 Silicon Wafer Preparation Process Flow 37

3.4 Source and Drain mask design and dimensions 38

3.5 Gate mask design and dimensions 39

3.6 Contacts mask design and dimensions 39

   

   

   

   

   

 

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xi

3.7 Metallization mask design and dimensions 40

3.8 ISFET device structure fabrication process flow 42 3.9 Surface modification and immobilization process of oligonucleotide

probes on the silicon nitride surface

47

4.1 Silicon nitride peak obtained with XRD 53

4.2 Source-Drain opening after etched with BOE (before stripping photoresist)

55

4.3 Source-Drain opening after etched with BOE (after stripping photoresist) (1)

55

4.4 Source-Drain opening after etched with BOE (after stripping photoresist) (2)

56

4.5 Wafer coated with phosphorus dopant before the diffusion process 57 4.6 Wafer diffused with the phosphorus dopant after the diffusion

process

57

4.7 Gate sensing membrane 58

4.8 Contact opening created on the ISFET 59

4.9 Over-etching of contact opening 60

4.10 Before removing photoresist after etching aluminium 61 4.11 After removing the photoresist that was protecting the aluminium

electrode

61

4.12 3D image of the gate sensing membrane obtained from AFM inspection

62

4.13 Surface roughness of silicon nitride gate thin film 63

4.14 Grain size of silicon nitride gate thin film 63

4.15 Individual diced ISFET device 65

4.16 Copper wires soldered onto the ISFET device and mounted on PCB stick

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xii

4.17 Prepared ISFET before pH testing (final product) 66 4.18 Equipment setup for electrical characterization 67

4.19 IV curves for pH2, pH3, pH7, pH8 and pH9 68

4.20 I/V curves of ISFET tested with different concentration of PBS in DI water

71

4.21 I/V curves of ISFET tested with different concentration of PBS in DI water (enlarged)

72

4.22 Plot of 𝑉𝑔 versus pH of ISFET 74

4.23 Before and after DNA immobilization and hybridization curves tested with PBS pH 7.2

76

4.24 ISFET hybridization with varying concentration of DNA targets 78  

   

   

   

   

   

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xiii

LIST OF ABBREVIATIONS

pH A measure of the acidity or alkalinity of a solution ISFET Ion-sensitive field-effect transistor

MOSFET Metal oxide semiconductor field-effect transistor BIOFET Biologically sensitive field-effect transistors GenFET DNA-modified FET

DNA-FET DNA-modified FET

ssDNA Single stranded deoxyribonucleic acid

CMOS Complementary metal–oxide–semiconductor DNA Deoxyribonucleic acid

PBS Phosphate Buffer Solution

AutoCAD Automated computer-aided design HPM High power microscope

AFM Atomic force microscopy

EDAX Energy dispersive x-ray spectroscopy XRD X-ray diffractometer

IV Current voltage characteristic

𝐼𝐷 Drain current

𝑉𝐷 Drain voltage

𝜇𝑛 Electron mobility of the channel

b Width of gate

L Length of gate

   

   

   

   

   

 

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xiv 𝐶𝑜 Oxide capacitance per unit area

𝑉𝑇 Threshold voltage

𝑉𝑔 Gate voltage

𝑉𝐷𝑆𝐴𝑇 Saturation voltage

Φ𝑀 work function between gate metal Φ𝑆𝑖 work function between silicon 𝑄𝑂𝑋 accumulated charge in the oxide

𝑄𝑆𝑆 accumulated charge in oxide-silicon interface 𝑄𝐵 depletion charge in the silicon

𝐸𝑟𝑒𝑓 constant potential of the reference electrode Ψ chemical input parameter

𝜒𝑠𝑜𝑙 surface dipole potential of the solvent

𝐻+ hydrogen ions

𝑆𝑖𝑂2 silicon dioxide 𝐴𝑙2𝑂3 aluminium(III) oxide 𝑇𝑎2𝑂5 tantalum pentoxide 𝐼𝑛2𝑂3 indium(III) oxide 𝑆𝑖3𝑁4 silicon nitride

HF Hydrofluoric acid

H2SO4 Sulfuric acid

N Nitrogen

CVD Chemical vapor deposition

Na+ Sodium ions

   

   

   

   

   

 

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xv

K+ Potassium ions

LOCOS Local oxidation of silicon

NH Amine group

UV Ultraviolet

SCE saturated calomel electrode Ag/AgCl silver-silver chloride

Hg Mercury

Cl Chloride

IC Integrated circuit

MOS Metal–oxide–semiconductor

OH Hydroxide

𝐶𝑎2+ Calcium ion

EnFET enzyme-modified FET

ImmunoFET immunologically modified FET CPFET cell-potential FET

IUPAC International Union of Pure and Applied Chemistry RNA ribonucleic acid

dsDNA double-stranded deoxyribonucleic acid

A Adenine

G Guanine

T Thymine

C Cytosine

VFB flat-band voltage  

   

   

   

   

   

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xvi N2 Nitrogen gas molecule

NH3 Ammonia

SSMCC sulfo-succinimidyl 4-(N-maleimidomethyl) cyclohexane- 1-carboxylate SNP single nucleotide polymorphism

PR Photoresist

Si Silicon

RCA1 Wafer cleaning solution RCA2 Wafer cleaning solution

DI Deionized

DC Direct Current

BOE Buffered Oxide Etch

NaOH Sodium hydroxide

APTES 3-aminopropyltriethoxysilane

𝑅𝑠 Sheet resistance

HCl Hydrochloric acid

H2 Hydrogen gas molecule

3D 3 dimensional

A-OH=SiOH Silanol group BH= SiNH2 Amine group

𝑆 Sensitivity

𝑉𝑡𝑕 Threshold voltage  

   

   

   

   

   

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xvii

LIST OF SYMBOLS

mV milivolt

°C Degree celcius

% Percentage

in. inches

min minute

Torr Gas pressure measurement unit

W Power measurement unit

nm Nanometer

µM Micro molar

g gram

ml mililiter

M mole

μL Microliter

Ω/sq Ohm per square

Å Angstrom

nm2 Nanometer square

% V/V Percentage of volume over volume  

   

   

   

   

   

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xviii

Pembangunan dan Fabrikasi Ion Sensitif Transistor (ISFET) Bagi Pengesanan pH, Immobilisasi dan Hibridisasi DNA

ABSTRAK

Fabrikasi ion sensitive transistor (ISFET) untuk pengesanan pH, immobilisasi dan hibridisasi DNA telah dilaporkan. Operasi ISFET adalah berdasarkan penyerapan cas pada permukaan membrane yang berinteraksi dengan larutan. Tesis ini menerangkan reka bentuk, fabrikasi dan pencirian ISFET untuk pengesanan pH, immobilisasi dan hibridisasi DNA.

Empat photomasks telah digunakan dalam proses fabrikasi untuk menghasilkan ISFET.

Peranti ISFET yang telah dihasilkan terlebih dahulu dibawa untuk pencirian morfologi diikuti dengan pencirian elektrik. Untuk analisis ISFET dalam larutan kajian, elektrod Ag / AgCl telah digunakan sebagai elektrod rujukan dan direndam dalam larutan pH yang berbeza. Keputusan yang dihasilkan oleh system pengukuran LabTracer 2.0 telah menunjukkan bahawa ciri IV peranti ISFET memberikan tindak balas linear. Larutan pH yang bersifat asid mengandungi ion H+ berupaya menarik lebih banyak elektron ke dalam saluran pengaliran untuk merendahkan rintangan dan memberikan nilai arus yang lebih tinggi. Larutan alkali pula menolak electron jauh daripada saluran pengaliran sekaligus meningkatkan rintangan dan oleh itu, nilai arus adalah lebih rendah. Apabila diuji dengan larutan fosfat (PBS), graf menunjukkan trend arus menjunam apabila kepekatan PBS yang diuji semakin berkurangan. Adalah didapati bahawa peranti ISFET yang telah diuji mempunyai sensitiviti 43.13 mV/pH. Peranti ISFET telah menjalani proses DNA selepas pencirian elektrik dengan pH dan PBS. Immobilisasi dan hibridisasi DNA telah dikesan melalui nilai arus yang semakin menurun. Sebelum proses immobilisasi DNA dilakukan ke atas ISFET, permukaan silikon nitrat telah diubahsuai dengan tindak balas kimia untuk membolehkan membran ISFET untuk bergabung dengan probe DNA. Ia juga didapati bahawa penurunan kepekatan sasaran DNA dalam proses hibridisasi telah menyumbang kepada penurunan arus yang dikesan. Sebagai kesimpulan, ISFET silikon nitrat adalah peranti fleksibel yang boleh digunakan untuk mengesan pH dan juga untuk immobilisasi dan hibridisasi DNA.

   

   

   

   

   

 

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xix

Development and Fabrication of Ion Sensitive Field Effect Transistor (ISFET) for pH Detection, DNA Immobilization and Hybridization

ABSTRACT

The fabrication of ion sensitive field-effect transistor (ISFET) using silicon nitride (Si3N4) as the sensing membrane is reported. The operation of ISFET is based on the surface charge adsorption of the membrane-solution interface. This thesis describes the design, fabrication and characterization of ISFET for pH detection, DNA immobilization and hybridization. Four photomasks were utilized in the fabrication process to create the ISFET device. The fabricated ISFET device was first brought to morphological characterization before proceeding with the electrical characterization. For the analysis of ISFET in test solution, the Ag/AgCl electrode was used as the reference electrode immersed in different values pH buffer. The results were generated by LabTracer 2.0 measurement system which shows that IV characteristic of ISFET devices gives linear response. The acidic pH buffers contains H+ ions which attract more electron into the conduction channel lowering the channel resistance giving higher value of current flow.

While the alkaline pH buffers contains OH- ions which pushed away the electrons from the conduction channel generating more positive holes increasing the channel resistance, thus giving a lower value of current flow. When tested with phosphate buffer solution (PBS), the curves show a decreasing trend of drain current with decreasing concentration of the PBS. It was found that the device has a sensitivity of 43.13 mV/pH. The ISFET device has undergo DNA processes after the electrical characterization with pH and PBS. The DNA immobilization and hybridization processes were detected through a drop in the drain current of the device. Prior to DNA immobilization, the silicon nitride surface was chemically modified to enable the ISFET sensing membrane for DNA probes coupling. It was also observed that with decreasing concentration of DNA complimentary targets in the hybridization process has contributed to the decreasing drain current detected. As a conclusion, the silicon nitride ISFET is a flexible device which can be used to detect pH as well as to perform DNA immobilization and hybridization.

   

   

   

   

   

 

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1 CHAPTER 1

BACKGROUND

1.1 Introduction

In daily life, the pH plays an important role in human activities. The pH appears whenever other substances are diluted with water, specifically called a solution. The pH refers to the measure of the amount of hydrogen ions present in a solution. Solutions with pH lower than 7 are categorized as acidic while solutions with pH higher than 7 are said to be alkaline. The measurement of pH in a solution can be performed by a few methods.

However, conservative ways of measuring pH is not very convenient which leads to the invention of a new device. The ISFET was invented by Bergveld in 1970 and was the first miniaturized silicon based chemical sensor. His work has shown that by omitting the metal gate from a MOSFET and leaving the oxide layer beneath to be exposed to a solution, the characteristics of the device are then affected by the ionic activities of the solution (Bergveld, 1970). This device gives plenty of advantages such as small size and weight, high reliability, fast response and low cost mass production. Moreover, it‘s possible field of applications varies from medicine, biotechnology, food industries, environmental monitoring and many more.

A BIOFET can be constructed from an ISFET by modifications made to the gate material as the ISFET allows the integration with biological element. These devices utilize the charge effect to transduce the recognizing phenomena of the DNA target probes bind with its complementary. In this project, the Genetic Field-Effect Transistor (GenFET) or  

   

   

   

   

   

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better known as DNA-FET was fabricated. This device was made possible by immobilizing well defined sequences of single strand DNA (ssDNA) onto a transducer, which converts the specific recognition process of two DNA single strands through the hybridization event into measurable signal (Schöning & Poghossian, 2002). In this research, devices are produced to perform both pH measuring and DNA immobilization and hybridization process.

1.2 Problem Statement

There are some traditional pH measuring methods in the market such as the litmus papers and glass pH electrodes. These measuring methods are simple and giving considerably quick measurement results. However, they do have their disadvantages.

Litmus papers rely on color indication which is not convenient for people with color blind difficulties. Moreover, litmus papers are not reusable after each use. Litmus papers also cannot be used for continuous monitoring of a process as it can be attacked by process solutions which can interfere the color change (Atkins & Paula, 1978). On the other hand, glass pH electrodes too are bulky and fragile. It also faces the risk of breaking and it is avoided in food industries. Glass pH electrodes cannot operate at temperature higher than 60°C (Vonau & Guth, 2006). It requires frequent maintenance and high setup cost. Unlike the other pH measuring methods, ISFET is reusable, fast response, small in size and light in weight.

The material on the gate of an ISFET is a very important factor that determines the pH sensitivity of the device itself. The material of the gate must be able to detect specific ions of the sample test solutions, avoid hydration and prevent ion migration to the  

   

   

   

   

   

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semiconductor layer (Cane, Gracia, & Merlos, 1997). Many researchers have been working on inorganic oxides as silicon dioxide has been identified as inadequate to function as pH sensing membrane. They have been experimenting with inorganic oxides in their works (Matsuo et al., 1981; Akiyama et al., 1982; Chan et al., 1987; Wong et al., 1989; Gimmel et al., 1989; Vlasov et al., 1990). Of the materials investigated, silicon nitride was found to

be suitable as pH sensitive membrane with acceptable results (Matsuo et al., 1981).

Therefore, silicon nitride is the good choice for ISFET considering it is also a material easily found in CMOS process foundries.

Considering both factors above, it has brought to the idea of fabricating a device that is able to perform both pH measurement and DNA detection. Current devices fabricated are normally made for single specific function. For this purpose, the silicon nitride has been chosen as the gate material as it allows DNA probes immobilization too, providing that some chemical modifications are made to its surface.

1.3 Research Objectives

The aim of this research is to design, fabricate and characterize ISFET based biosensor for DNA immobilization and hybridization process. The characterization will involve both surface morphological and electrical analysis to investigate the device working mechanism and also its sensitivity.

However, the specific objectives of this research are:

i. To study the ISFET device fabrication process using the revolutionized self-aligned method for MOSFET.

   

   

   

   

   

 

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ii. To understand the working principles of ISFET and the mechanism of DNA immobilization and hybridization

iii. To evaluate the ISFET electrical characteristics using the IV system by testing with pH buffer solutions and phosphate buffer solution (PBS).

iv. To study the DNA immobilization and hybridization processes on ISFET silicon nitride gate.

v. To evaluate the ISFET device before and after DNA immobilization and hybridization.

1.4 Research Scopes

This research is embarked based on the following scopes:

i. To design four masks which include the source-drain mask, gate mask, contact mask and metallization mask. These masks will be designed by using AutoCAD tool and then printed on transparency sheets as the precision of the measurement is not the main concern of this project.

ii. To fabricate the ISFET device as the basic structure for DNA immobilization process. The device will be fabricated using the revolutionized self-aligned process for MOSFET.

iii. To characterize the optical and physical characteristic of silicon nitride gate by using high power microscope (HPM), atomic force microscopy (AFM), energy dispersive x-ray spectroscopy (EDAX), and x-ray diffractometer (XRD).

   

   

   

   

   

 

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iv. To perform electrical characterization on ISFET using the IV curve technique with pH buffer solutions and phosphate buffer solution (PBS).

v. To perform surface modification, DNA immobilization and hybridization on the silicon nitride gate surface.

vi. To inspect the effect of DNA complimentary target concentration on ISFET.

1.5 Thesis Organization

This thesis consists of 5 chapters. Chapter 1 gives a general idea of the research to readers through the introduction, problem statement, objectives, significance of the project and project scopes.

Chapter 2 is the literature review which explains the fundamental theories of the working principles, device structure, device sensing layer properties and potential applications.

Chapter 3 describes the mask designs and mask dimensions, the ISFET fabrication processes, surface modification on silicon nitride using chemical solutions as well as DNA immobilization and hybridization procedures.

Chapter 4 contains the results obtained and data analysis of the research. The data obtained were tabulated and plotted into graphs for analysis. Discussion and explanation based on the results are presented in this chapter.

Last but not least, Chapter 5 summarizes the thesis findings based on the objectives that are set for this research and also some recommendation for future works to improvise the current device performance.

   

   

   

   

   

 

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