Biomolecular Computation for... | Buy

Computers built with moleware? The drive toward non-silicon computing is underway, and this first-of-its-kind guide to molecular computation gives researchers 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.

Katsunori Shimohara is a professor in the Department of Information Systems Design, Faculty of Engineering, Doshisha University in Kyoto, Japan.

Preface	p. xi
Introduction: How to Go Beyond Traditional Computers	p. 1
Scientific Motivation Versus the Needs of the IT Industry	p. 3
Cutting-Edge Technologies for Building a Molecular Computer: From Nanobioscience and Nanotechnology to Nanobioinformatics	p. 5
Synthetic Biology	p. 6
Emerging Technologies for Protein Analysis: To Gain Information about Proteins, Protein Interaction, and Their Links to the Medicine	p. 8
Preliminaries in Nanobioscience	p. 9
Gedanken Model	p. 10
Some Concepts in Biochemistry	p. 11
Systems Biology	p. 12
Perspectives on Innovative Technologies for Biomolecular Computing: Benefits from Breakthroughs of Molecular Biology in the New Millennium	p. 12
Challenges from Real-World Applications	p. 13
Performances of Biomolecular Computing	p. 13
Technological Difficulties on Feasibility of Implementation of a Biomolecular Computer: Scalability, Reliability, and Controllability	p. 13
Back to Molecular Informatics: How to Use Molecules to Represent Information	p. 15
References	p. 19
The State-of-the-Art Molecular Biology and Nanotechnology	p. 23
Genomics	p. 23
Proteomics	p. 26
Cellular Structure from the Viewpoint of Molecular Biology	p. 29
Cell as a Nanobiomachine	p. 31
Moleware Mechanics for Cellular Nanobiomachine: Molecules Carrying Messages	p. 33
Molecular Informatics for Cellular Nanobiomachine	p. 34
Signal Transduction and Signaling Pathways of Cells	p. 35
The Link Between the Signaling Pathway and Molecular Movement	p. 37
The Links Between Signal Pathways and Neuron Function	p. 37
Measurement and Detection in Material Science: Towards Manipulation of Biological Molecules	p. 38
Pharmaceutical Nanobioinformatics	p. 41
"Naive" Thinking for Pharmaceutics	p. 41
Molecular Information Flow as a Possible Solution Towards Potential Application of Nanobioinformation Processing Systems	p. 42
References	p. 45
Nanobiomachines for Information Processing and Communication: Exploring Fundamental Principles of NanobioICT	p. 49
Mission of NanobioICT	p. 50
Information Theory of NanobioICT: Shannon Meets Feynman	p. 53
Embryonic Approaches to NanobioICT	p. 56
A Glance at Informatics of Moleware Communication	p. 67
An Informatics Form of a Molecular Viterbi Algorithm	p. 76
Network Coding in Molecular Informatics	p. 80
Quadruple Convergence	p. 84
References	p. 87
Computing by Biomoleware: Diverse Methods from Diversified Materials	p. 91
How to Build an Engineered Computational Nanobiosystem: Inspiration from Existing Nanobiomachines in Nature	p. 92
Nanobioworld Becomes Observable with the Help of Innovative Measurement Technology: Schrodinger's Cat Is at the Door	p. 92
Seeking a Movable Nanobiomachine: Postman in Moleware	p. 94
Methodology Learned from the Cell and Beyond	p. 96
Information Processing in Artificial Nanobiosystems: An Odyssey Beyond the Blind Watchmaker	p. 97
Molecular Complex as Memory-Memorizing Instead of Braining	p. 100
Molecular Clock-The Heart of Synchronous Moleware	p. 105
Moleware Coding in Nanobiomachine-A Solution from the Cell	p. 108
Computing by Nucleic Acids	p. 114
DNA Computing	p. 115
RNA Computing	p. 121
Surface-Based DNA Computing	p. 123
Nanobiotechnology for DNA Computing	p. 125
Computing by Biochemical Reactions in Microbes	p. 127
Information Processing Mechanism of Microbes	p. 127
Computing by Gene Operations in Ciliates	p. 129
Moleware Microarray	p. 132
References	p. 136
Theoretical Biomolecular Computing	p. 141
Basic Concepts in Computer Science for Molecular Computing	p. 142
Formal Language	p. 143
Automata	p. 145
Formalized Molecular Computing	p. 146
H-System	p. 147
P-System	p. 150
Rediscovering the Informatics Structure of the Biomolecular Computing System: An Informatics View of the Formal Processes of the Biomolecular Computing H-System	p. 153
How to Design Algorithms for a Molecular Computer	p. 157
Observing Complexity from Benchmarks	p. 157
Obtaining Efficiency from Pathway Designs: Algorithmic Design Through Examples	p. 160
Touchstone for Nanobio-Oracle: Moleware Logic	p. 171
Consistency of Computing Operators and Feasible Experimental Supports: Verification of Logic Process	p. 171
Formalized Method for Moleware Logic	p. 173
References	p. 179
Cellular Biomolecular Computing Based on Signaling Pathways: Kinase Computing	p. 181
Cellular Pathway: Another Ubiquitous Society in Another Universe	p. 182
Ubiquitous Cell Communication for Parallel Information Processing	p. 182
The Molecular Switch as a Bridge Between Cell Communication and Molecular Computing	p. 184
Binary Information Representation by Molecular Switch	p. 185
Computing Formalized as an Automaton	p. 188
Example: Designing an Automaton for Kinase Switches Guided by GTPase	p. 190
Information Structure for Automaton-Based Computing	p. 191
A Computing Model Based on Pathway Units with Turing Computability	p. 193
From Automaton to Rewriting: Toward General Parallel Computing	p. 199
Formalization	p. 199
Transition from Hypergraphs to Bigraphs	p. 203
McNaughton Language, Confluent Rewriting, and Controlling with the Structural Characteristics of MSP-Automaton	p. 205
Designing a Rewriting Process by Pathway Units Based on MSP-Automata	p. 209
A Compiler: Translating Moleware Language into Programmer-Friendly Informatics Operators	p. 210
Systematically Understanding the Interaction Structure in Pathway Computing	p. 212
Generalized Form for Computing	p. 212
Blueprint of a Kinase Computer	p. 214
Quantitative Description for Biochemical Features	p. 214
Materials for Information Processing	p. 217
Controllability Under Protocols in Bioinformation	p. 218
References	p. 221
Comparison of Algorithms for Biomolecular Computing and Molecular Bioinformatics	p. 223
Formal Characteristics of Algorithms for Biomolecular Computing	p. 224
DNA Computing	p. 225
Surface-Based DNA Computing	p. 225
H-Systems	p. 225
P-Systems	p. 226
DNA Computing Method by Ciliates	p. 226
Interactions in Molecular Bioinformatics Algorithms	p. 227
Example 1: Interaction of GTPases	p. 229
Example 2: Interaction of Kinases/Phosphatases	p. 232
Common Points of Biomolecular Computing and Molecular Bioinformatics for Algorithms	p. 239
Example: Describing Cellular Pathways by Graph Rewriting	p. 242
Exploring Logical Description for Molecular Bioinformatics Based on Formalization and Abstract Operations	p. 245
References	p. 250
Emerging Nanobiotechnology in Multiple Disciplines	p. 253
The Tale of Two Media: Molecular Electricity and Biomolecular Signaling	p. 253
How Small Can an Information Processing System Be Made?	p. 254
Informatics of Porphyrin Systems	p. 255
Transition from the Supporting Points to Integrations of Different Aspects of Molecular Information Processing	p. 260
Cell Communication for Engineering Purpose	p. 263
From Bit Level of Information Representation to Observe Cellular Communication	p. 265
The Biophysical Effectors of the Molecular Information Flow	p. 266
Effects of Molecular Protocols by the Internal Components of Cells	p. 266
Control Nodes in Moleware Communication Networks	p. 267
Collision-Avoid: An Issue on Efficiency of Moleware Communication in Cells	p. 268
References	p. 272
About the Authors	p. 275
Index	p. 277
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