UNIVERSITI PUTRA MALAYSIA MODELING OF STATIC AND …psasir.upm.edu.my/id/eprint/32017/1/FSKTM 2012 13R.pdf · set baru wajaran optimum struktur sifat fullerenes C 60 dan C 70. Fullerene

UNIVERSITI PUTRA MALAYSIA

MODELING OF STATIC AND DYNAMIC COMPONENTS OF BIO-NANOROBOTIC SYSTEMS

HAMIDREZA KHATAEE GAVGANI

FSKTM 2012 13

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MODELING OF STATIC AND DYNAMIC COMPONENTS OF

BIO-NANOROBOTIC SYSTEMS

By


Thesis Submitted to the School of Graduate Studies, Universiti Putra

Malaysia in Fulfilment of the Requirements for the Degree of Master

of Science

July 2012

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DEDICATION

To

My parents, Jamshid and Rouhiyeh, for their love, support, and understanding.

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Abstract of thesis presented to the Senate of Universiti Putra Malaysia

in fulfilment of the requirement for the degree of Master of Science

MODELING OF STATIC AND DYNAMIC COMPONENTS OF

BIO-NANOROBOTIC SYSTEMS

By


July 2012

Chair: Teh Noranis Mohd Aris, PhD

Faculty: Computer Science and Information Technology

Computational modeling techniques can facilitate to achieve in applications of

biological nanocomponents for the development of potential bio-nanorobotic systems

through representing the properties of these components. This work focuses on the

current library of components for the development of bio-nanorobots and considers

the recently reported static (e.g. C60 and C70 fullerenes) and dynamic (e.g. kinesin

and muscle myosin nanomotors) components for modeling. This thesis proposes two

new computational techniques to model these static and dynamic components.

The first modeling technique applies graph algorithms to compute a new set of

optimal weighted structural properties of C60 and C70 fullerenes. C60 and C70

fullerene nanoparticles are composed of 60 and 70 equivalent carbon atoms,

respectively, arranged as hollow cages. In this technique, the graph-based structural

models of the fullerenes are proposed using their real structural information. Then,

these graph-based structural models of the fullerenes and graph algorithms based on

dynamic programming are applied to compute a new set of optimal weighted

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physical properties of the components including Wiener, hyper-Wiener, Harary and

reciprocal Wiener indices as well as Hosoya and hyper-Hosoya polynomials. In

addition, a graph algorithm based on greedy methods is employed to compute a new

set of optimal weighted electronic properties of the fullerenes via computing their

Minimum Weight Spanning Trees (MWSTs). The computed optimal weighted

physical and electronic properties of the fullerenes showed a good agreement with

the mathematics of the properties as well as the principles of the employed graph

algorithms.

The second modeling technique applies agent technology to propose comprehensive

structural and behavioral models of kinesin and muscle myosin protein nanomotors

that can introduce the nanomotors as autonomous and intelligent nanosystems. In this

technique, kinesin and muscle myosin nanomotors are introduced as physical

intelligent agents. Agent-based structural models of the nanomotors are proposed

using composite diagram of Unified Modeling Language (UML) to introduce the

sensors and actuators of the nanomotors. Moreover, agent-based behavioral models

of the nanomotors are developed using state machine diagrams of UML to illustrate

the internal autonomous and intelligent decision-making processes of the

nanomotors. The agent-based behavioral state machine models of the nanomotors are

validated with comparing their mathematical definitions, developed as Deterministic

Finite Automatons (DFAs) and their respective grammars, to the natural behaviors of

the nanomotors. Finally, the behavioral DFA models of the nanomotors are

implemented as their software agent models. Accordingly, the outputs of the

software agent models were in good agreement with the natural behaviors of the

nanomotors.

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Abstrak tesis yang dikemukakan kepada Senat Universiti Putra Malaysia

sebagai memenuhi keperluan untuk ijazah Master Sains

PEMODELAN KOMPONEN STATIK DAN DINAMIK

SISTEM BIO-NANOROBOTIK

Oleh


Julai 2012

Pengerusi: Teh Noranis Mohd Aris, PhD

Fakulti: Sains Komputer dan Teknologi Maklumat

Teknik pemodelan pengkomputeran boleh membantu aplikasi biologikal

nanokomponen untuk pembangunan bagi meningkatkan potensi sistem bio-

nanorobotik melalui sifat komponen ini. Tumpuan kerja diberikan kepada komponen

perpustakaan semasa dalam pembangunan bio-nanorobotik dan mengambilkira

laporan statik terkini (seperti fullerenes C60 dan C70) dan komponen dinamik (seperti

kinesin dan otot myosin nanomotors) di dalam pemodelan komponen ini. Tesis ini

mencadangkan dua teknik pengkomputeran baru untuk memodelkan komponen

statik dan dinamik.

Teknik pemodelan pertama mengaplikasikan algorithma grafik untuk mengira satu

set baru wajaran optimum struktur sifat fullerenes C60 dan C70. Fullerene

nanoparticles C60 dan C70 terdiri daripada 60 dan 70 atom karbon yang masing-

masing setara dan disusun sebagai sangkar berongga. Di dalam teknik ini, struktur

model fullerenes berasaskan graf menggunakan maklumat struktur sebenar mereka

dicadangkan. Kemudian, struktur model fullerenes berasaskan graf dan algoritma

graf berdasarkan pengaturcaraan dinamik digunakan untuk mengira satu set baru

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wajaran optimum sifat fizikal komponen termasuklah Wiener, hyper-Wiener, Harary

dan salingan indeks Wiener serta Hosoya dan polinomial hyper-Hosoya. Di samping

itu, algoritma graf yang berasaskan kaedah tamak digunakan untuk mengira satu set

baru wajaran optimum sifat elektronik fullerenes melalui pengiraan Minimum Weight

Spanning Tress (MWSTs). Pengiraan wajaran optimum sifat fizikal dan elektronik

fullerenes menunjukkan satu keserasian yang baik dengan sifat-sifat matematik serta

prinsip algoritma graf yang digunakan.

Teknik pemodelan kedua menggunakan teknologi ejen bagi mencadangkan struktur

dan tingkah laku model kinesin dan otot myosin nanomotors protein yang

komprehensif yang mana dapat memperkenalkan nanomotors sebagai autonomi dan

nanosistem yang cerdik. Di dalam teknik ini, kinesin dan otot myosin nanomotors

diperkenalkan sebagai ejen fizikal pintar. Struktur model nanomotors berasaskan

ejen dicadangkan menggunakan rajah komposit Unified Modeling Language (UML)

untuk memperkenalkan penderia dan penggerak nanomotors. Selain itu, model

tingkah laku nanomotors berasaskan ejen dibangunkan menggunakan rajah UML

state machine bagi menggambarkan autonomi dalaman dan proses pembuatan

keputusan cerdik nanomotors. Model nanomotors berasaskan ejen tingkah laku state

machine telah disahkan dengan membandingkan definisi matematik mereka,

dibangunkan sebagai Deterministic Finite Automatons (DFAs) menggunakan

tatabahasa tertentu, kepada tingkah laku semulajadi nanomotors. Akhir sekali,

tingkah laku model DFA nanomotors dilaksanakan sebagai model ejen

perisian. Sehubungan dengan itu, output bagi model ejen perisian dibuktikan sangat

serasi dengan tingkah laku semulajadi nanomotors.

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ACKNOWLEDGEMENTS

First of all I would like to thank my supervisory committee, Dr. Teh Noranis Mohd

Aris and Assoc. Prof. Dr. Md. Nasir Sulaiman, for giving me the opportunity to work

under their supervision. I wish to express my sincere thanks to their guidance,

support and advice throughout this work.

I would also like to express my thanks to the staff of Faculty of Computer Science

and Information Technology, Universiti Putra Malaysia. Moreover, my sincere

thanks go to my friends who have helped me in my research work.

In particular, I would like to expressly thank my family, especially my parents, for

their love, support and understanding throughout my study.

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I certify that a Thesis Examination Committee has met on 25 July 2012 to conduct

the final examination of Hamidreza Khataee Gavgani on his thesis entitled

“Modelling of Static and Dynamic Components of Bio-Nanorobotic Systems” in

accordance with the Universities and University Colleges Act 1971 and the

Constitution of the Universiti Putra Malaysia [P.U.(A) 106] 15 March 1998. The

Committee recommends that the student be awarded the Master of Science.

Members of the Thesis Examination Committee were as follows:

Nur Izura Udzir, PhD

Associate Professor

Faculty of Computer Science and Information Technology

Universiti Putra Malaysia

(Chairman)

Masrah Azrifah Azmi Murad, PhD

Associate Professor



(Internal Examiner)

Razali Yaakob, PhD

Senior Lecturer



(Internal Examiner)

Zulaiha Ali Othman, PhD

Associate Professor

Faculty of Information Science and Technology

Universiti Kebangsaan Malaysia

Malaysia

(External Examiner)

SEOW HENG FONG, PhD

Professor and Deputy Dean

School of Graduate Studies

University Putra Malaysia

Date:

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This thesis was submitted to the Senate of University Putra Malaysia and has been

accepted as fulfilment of the requirement for the degree of Master of Science. The

members of the Supervisory Committee were as follows:

Teh Noranis Mohd Aris, PhD

Senior Lecturer



(Chairman)

Md. Nasir Sulaiman, PhD

Associate Professor



(Member)

BUJANG BIN KIM HUAT, PhD

Professor and Dean

School of Graduate Studies

University Putra Malaysia

Date:

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DECLARATION

I declare that the thesis is my original work except for quotations and citations which

have been duly acknowledged. I also declare that it has not been previously, and is

not currently, submitted for any other degree at University Putra Malaysia or at any

other institution.


Date: 25 July 2012

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TABLE OF CONTENTS

Page

ABSTRACT iii

ABSTRAK v

ACKNOWLEDGEMENTS vii

APPROVAL viii

DECLARATION x

LIST OF TABLES xiii

LIST OF FIGURES xiv

LIST OF ABBREVIATIONS xv

CHAPTER

1 INTRODUCTION 1

1.1 Background 1

1.2 Problem Statement 4

1.3 Research Objective 6

1.4 Research Scope 7

1.5 Research Contribution 8

1.6 Organization of Thesis 9

2 LITERATURE REVIEW 11

2.1 Introduction 11

2.2 Static Components 12

2.2.1 C60 Fullerene Nanoparticle 12

2.2.2 C70 Fullerene Nanoparticle 14

2.2.3 Mathematics of Optimal Physical Properties 15

2.2.4 Related Computational Works 18

2.3 Dynamic Components 20

2.3.1 Kinesin Nanomotor 21

2.3.2 Muscle Myosin Nanomotor 24

2.3.3 Related Computational Works 28

2.4 Summary 30

3 RESEARCH METHODOLOGY 31

3.1 Introduction 31

3.2 Modeling Technique of Static Components 31

3.3 Modeling Technique of Dynamic Components 34

3.4 Summary 36

4 DESIGN AND IMPLEMENTAION OF THE PROPOSED MODELING

SYSTEMS 37

4.1 Introduction 37

4.2 Basic Concepts 38

4.2.1 Graph Algorithms 38

4.2.2 Agent Technology 39


4.3.1 Graph-Based Structural Models 43

4.3.2 Computing Optimal Weighted Physical and Electronic Properties 46

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4.4.1 Dynamic Components as Physical Agents 52

4.4.2 Agent-based Modeling of the Dynamic Components 54

4.4.2.1 Kinesin Nanomotor 55

4.4.2.2 Muscle Myosin Nanomotor 68

4.5 Summary 79

5 RESULTS AND DISCUSSION 81

5.1 Introduction 81


5.2.1 Optimal Weighted Physical and Electronic Properties of C60

Nanoparticle 82

5.2.2 Optimal Weighted Physical and Electronic Properties of C70

Nanoparticle 88


5.3.1 Generated Actions of the Software Agent Model of Kinesin

Nanomotor 96

5.3.2 Generated Actions of the Software Agent Model of Muscle Myosin

Nanomotor 98

5.4 Summary 100

6 CONCLUSIONS AND FUTURE WORKS 102

6.1 Conclusions 102

6.2 Future Works 107

REFERENCES 109

BIODATA OF STUDENT 115

LIST OF PUBLICATIONS 116

Documents

UNIVERSITI PUTRA MALAYSIA MODELING OF STATIC AND …psasir.upm.edu.my/id/eprint/32017/1/FSKTM 2012 13R.pdf · set baru wajaran optimum struktur sifat fullerenes C 60 dan C 70. Fullerene