UNIVERSITI PUTRA MALAYSIA MODELING OF STATIC AND …psasir.upm.edu.my/id/eprint/32017/1/FSKTM 2012...
Transcript of UNIVERSITI PUTRA MALAYSIA MODELING OF STATIC AND …psasir.upm.edu.my/id/eprint/32017/1/FSKTM 2012...
UNIVERSITI PUTRA MALAYSIA
MODELING OF STATIC AND DYNAMIC COMPONENTS OF BIO-NANOROBOTIC SYSTEMS
HAMIDREZA KHATAEE GAVGANI
FSKTM 2012 13
© COPYRIG
HT UPM
MODELING OF STATIC AND DYNAMIC COMPONENTS OF
BIO-NANOROBOTIC SYSTEMS
By
HAMIDREZA KHATAEE GAVGANI
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
© COPYRIG
HT UPM
ii
DEDICATION
To
My parents, Jamshid and Rouhiyeh, for their love, support, and understanding.
© COPYRIG
HT UPM
iii
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
HAMIDREZA KHATAEE GAVGANI
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
© COPYRIG
HT UPM
iv
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.
© COPYRIG
HT UPM
v
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
HAMIDREZA KHATAEE GAVGANI
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
© COPYRIG
HT UPM
vi
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.
© COPYRIG
HT UPM
vii
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.
© COPYRIG
HT UPM
viii
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
Faculty of Computer Science and Information Technology
Universiti Putra Malaysia
(Internal Examiner)
Razali Yaakob, PhD
Senior Lecturer
Faculty of Computer Science and Information Technology
Universiti Putra Malaysia
(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:
© COPYRIG
HT UPM
ix
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
Faculty of Computer Science and Information Technology
Universiti Putra Malaysia
(Chairman)
Md. Nasir Sulaiman, PhD
Associate Professor
Faculty of Computer Science and Information Technology
Universiti Putra Malaysia
(Member)
BUJANG BIN KIM HUAT, PhD
Professor and Dean
School of Graduate Studies
University Putra Malaysia
Date:
© COPYRIG
HT UPM
x
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.
HAMIDREZA KHATAEE GAVGANI
Date: 25 July 2012
© COPYRIG
HT UPM
xi
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 Static Components 43
4.3.1 Graph-Based Structural Models 43
4.3.2 Computing Optimal Weighted Physical and Electronic Properties 46
© COPYRIG
HT UPM
xii
4.4 Dynamic Components 52
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 Static Components 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 Dynamic Components 96
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