Biomolecular computation for bionanotechnology / Jian-Qin Liu, Katsunori Shimohara.

Format:

Book

Author/Creator:

Liu, Jian-Qin.

Contributor:

Shimohara, Katsunori.

Language:

English

Subjects (All):

Molecular computers.

Nanotechnology.

Biotechnology.

Physical Description:

xii, 286 pages : illustrations ; 27 cm

Place of Publication:

Boston : Artech House, [2007]

Summary:

Computers built with Moleware? The drive toward non-silicon computing is underway, and this first-of-its-kind guide to molecular computation gives practitioners a firm grasp of the technologies, biochemical details, and theoretical models at the cutting edge. It explores advances in molecular biology and nanotechnology and illuminates how the convergence of various technologies is propelling computational capacity beyond the limitations of traditional hardware technology and into the realm of moleware. With its wealth of models, algorithms, designs, and problem-solving applications, this volume is the first to bridge the gap between biomaterial sciences/molecular biology modeling and bioinformatics engineering for bionanoscale phenomena. It brings researchers up to speed on DNA computing and membrane computing, and describes nanobiomachines including Nanobio1CT and their potential in information processing and communications.

Contents:

Chapter 1 Introduction: How to Go Beyond Traditional Computers 1

1.1 Scientific Motivation Versus the Needs of the IT Industry 3

1.2 Cutting-Edge Technologies for Building a Molecular Computer: From Nanobioscience and Nanotechnology to Nanobioinformatics 5

1.2.1 Synthetic Biology 6

1.2.2 Emerging Technologies for Protein Analysis: To Gain Information about Proteins, Protein Interaction, and Their Links to the Medicine 8

1.3 Preliminaries in Nanobioscience 9

1.3.1 Gedanken Model 10

1.3.2 Some Concepts in Biochemistry 11

1.3.3 Systems Biology 12

1.3.4 Perspectives on Innovative Technologies for Biomolecular Computing: Benefits from Breakthroughs of Molecular Biology in the New Millennium 12

1.4 Challenges from Real-World Applications 13

1.4.1 Performances of Biomolecular Computing 13

1.4.2 Technological Difficulties on Feasibility of Implementation of a Biomolecular Computer: Scalability, Reliability, and Controllability 13

1.5 Back to Molecular Informatics: How to Use Molecules to Represent Information 15

Chapter 2 The State-of-the-Art Molecular Biology and Nanotechnology 23

2.1 Genomics 23

2.2 Proteomics 26

2.3 Cellular Structure from the Viewpoint of Molecular Biology 29

2.4 Cell as a Nanobiomachine 31

2.4.1 Moleware Mechanics for Cellular Nanobiomachine: Molecules Carrying Messages 33

2.4.2 Molecular Informatics for Cellular Nanobiomachine 34

2.5 Signal Transduction and Signaling Pathways of Cells 35

2.5.1 The Link Between the Signaling Pathway and Molecular Movement 37

2.5.2 The Links Between Signal Pathways and Neuron Function 37

2.6 Measurement and Detection in Material Science: Towards Manipulation of Biological Molecules 38

2.7 Pharmaceutical Nanobioinformatics 41

2.7.1 "Naive" Thinking for Pharmaceutics 41

2.7.2 Molecular Information Flow as a Possible Solution Towards Potential Application of Nanobioinformation Processing Systems 42

Chapter 3 Nanobiomachines for Information Processing and Communication: Exploring Fundamental Principles of NanobioICT 49

3.1 Mission of NanobioICT 50

3.2 Information Theory of NanobioICT: Shannon Meets Feynman 53

3.3 Embryonic Approaches to NanobioICT 56

3.4 A Glance at Informatics of Moleware Communication 67

3.5 An Informatics Form of a Molecular Viterbi Algorithm 76

3.6 Network Coding in Molecular Informatics 80

3.7 Quadruple Convergence 84

Chapter 4 Computing by Biomoleware: Diverse Methods from Diversified Materials 91

4.1 How to Build an Engineered Computational Nanobiosystem: Inspiration from Existing Nanobiomachines in Nature 92

4.1.1 Nanobioworld Becomes Observable with the Help of Innovative Measurement Technology: Schrodinger's Cat Is at the Door 92

4.1.2 Seeking a Movable Nanobiomachine: Postman in Moleware 94

4.1.3 Methodology Learned from the Cell and Beyond 96

4.2 Information Processing in Artificial Nanobiosystems: An Odyssey Beyond the Blind Watchmaker 97

4.2.1 Molecular Complex as Memory-Memorizing Instead of Braining 100

4.2.2 Molecular Clock-The Heart of Synchronous Moleware 105

4.2.3 Moleware Coding in Nanobiomachine-A Solution from the Cell 108

4.3 Computing by Nucleic Acids 114

4.3.1 DNA Computing 115

4.3.2 RNA Computing 121

4.3.3 Surface-Based DNA Computing 123

4.3.4 Nanobiotechnology for DNA Computing 125

4.4 Computing by Biochemical Reactions in Microbes 127

4.4.1 Information Processing Mechanism of Microbes 127

4.4.2 Computing by Gene Operations in Ciliates 129

4.4.3 Moleware Microarray 132

Chapter 5 Theoretical Biomolecular Computing 141

5.1 Basic Concepts in Computer Science for Molecular Computing 142

5.1.1 Formal Language 143

5.1.2 Automata 145

5.2 Formalized Molecular Computing 146

5.2.1 H-System 147

5.2.2 P-System 150

5.2.3 Rediscovering the Informatics Structure of the Biomolecular Computing System: An Informatics View of the Formal Processes of the Biomolecular Computing H-System 153

5.3 How to Design Algorithms for a Molecular Computer 157

5.3.1 Observing Complexity from Benchmarks 157

5.3.2 Obtaining Efficiency from Pathway Designs: Algorithmic Design Through Examples 160

5.4 Touchstone for Nanobio-Oracle: Moleware Logic 171

5.4.1 Consistency of Computing Operators and Feasible Experimental Supports: Verification of Logic Process 171

5.4.2 Formalized Method for Moleware Logic 173

Chapter 6 Cellular Biomolecular Computing Based on Signaling Pathways: Kinase Computing 181

6.1 Cellular Pathway: Another Ubiquitous Society in Another Universe 182

6.1.1 Ubiquitous Cell Communication for Parallel Information Processing 182

6.2 The Molecular Switch as a Bridge Between Cell Communication and Molecular Computing 184

6.2.1 Binary Information Representation by Molecular Switch 185

6.2.2 Computing Formalized as an Automaton 188

6.2.3 Example: Designing an Automaton for Kinase Switches Guided by GTPase 190

6.2.4 Information Structure for Automaton-Based Computing 191

6.2.5 A Computing Model Based on Pathway Units with Turing Computability 193

6.3 From Automaton to Rewriting: Toward General Parallel Computing 199

6.3.1 Formalization 199

6.3.2 Transition from Hypergraphs to Bigraphs 203

6.3.3 McNaughton Language, Confluent Rewriting, and Controlling with the Structural Characteristics of MSP-Automaton 205

6.3.4 Designing a Rewriting Process by Pathway Units Based on MSP-Automata 209

6.3.5 A Compiler: Translating Moleware Language into Programmer-Friendly Informatics Operators 210

6.3.6 Systematically Understanding the Interaction Structure in Pathway Computing 212

6.3.7 Generalized Form for Computing 212

6.4 Blueprint of a Kinase Computer 214

6.4.1 Quantitative Description for Biochemical Features 214

6.4.2 Materials for Information Processing 217

6.4.3 Controllability Under Protocols in Bioinformation 218

Chapter 7 Comparison of Algorithms for Biomolecular Computing and Molecular Bioinformatics 223

7.1 Formal Characteristics of Algorithms for Biomolecular Computing 224

7.1.1 DNA Computing 225

7.1.2 Surface-Based DNA Computing 225

7.1.3 H-Systems 225

7.1.4 P-Systems 226

7.1.5 DNA Computing Method by Ciliates 226

7.2 Interactions in Molecular Bioinformatics Algorithms 227

7.2.1 Example 1: Interaction of GTPases 229

7.2.2 Example 2: Interaction of Kinases/Phosphatases 232

7.3 Common Points of Biomolecular Computing and Molecular Bioinformatics for Algorithms 239

7.3.1 Example: Describing Cellular Pathways by Graph Rewriting 242

7.4 Exploring Logical Description for Molecular Bioinformatics Based on Formalization and Abstract Operations 245

Chapter 8 Emerging Nanobiotechnology in Multiple Disciplines 253

8.1 The Tale of Two Media: Molecular Electricity and Biomolecular Signaling 253

8.2 How Small Can an Information Processing System Be Made? 254

8.3 Informatics of Porphyrin Systems 255

8.4 Transition from the Supporting Points to Integrations of Different Aspects of Molecular Information Processing 260

8.5 Cell Communication for Engineering Purpose 263

8.5.1 From Bit Level of Information Representation to Observe Cellular Communication 265

8.5.2 The Biophysical Effectors of the Molecular Information Flow 266

8.5.3 Effects of Molecular Protocols by the Internal Components of Cells 266

8.5.4 Control Nodes in Moleware Communication Networks 267

8.5.5 Collision-Avoid: An Issue on Efficiency of Moleware Communication in Cells 268.

Notes:

Includes bibliographical references and index.

ISBN:

1596930144

9781596930148

OCLC:

77485778