22 18 An Overview of DNA‐Based Digital Data Storage 18.1 Introduction 18.2 Components of a DNA Storage System 18.3 Conclusions and Outlook Acknowledgments References
23 19 Interfacing Enzyme‐Based and DNA‐Based Computing Systems: From Simple Boolean Logic to Sophisticated Reversible Logic Systems 19.1 Interfacing Enzyme‐Based and DNA‐Based Computing Systems is a Challenging Goal: Motivations and Approaches 19.2 Bioelectronic Interface Transducing Logically Processed Signals from an Enzymatic System to a DNA System 19.3 The Bioelectronic Interface Connecting Enzyme‐Based Reversible Logic Gates and DNA‐Based Reversible Logic Gates: Realization in a Flow Device 19.4 Enzyme‐Based Fredkin Gate Processing Biomolecular Signals Prior to the Bioelectronic Interface 19.5 Reversible DNA‐Based Feynman Gate Activated by Signals Produced by the Enzyme‐Based Fredkin Gate 19.6 Conclusions and Perspectives 19.A Appendix References
24 20 Conclusions and Perspectives: Further Research Directions and Possible Applications
25 Index
List of Tables
1 Chapter 2Table 2.1 The sequence of extraction operations for a given illustrative SAT ...
2 Chapter 5Table 5.1 List of some common RNA aptamers with corresponding fluorogenic lig...
3 Chapter 10Table 10.1 Principal characteristics of the three experimental systems capabl...
4 Chapter 12Table 12.1 Truth table of various basic logic gates.Table 12.2 General classification of different advanced DNA logic circuits.
5 Chapter 14Table 14.1 Paths and values encoded by the different test tubes used for solv...
6 Chapter 17Table 17.1 Comparison of conventional fluorescence and nanopore decoding meth...
List of Illustrations
1 Chapter 1Figure 1.1 Moore's law – exponential increase of transistors on integrated c...Figure 1.2 Biomolecular computing systems mimicking operation of different B...Figure 1.3 The discoverers of the structure of DNA. James Watson (b.1928) at...Figure 1.4 The structure of the DNA double helix. The atoms in the structure...Figure 1.5 Leonard Adleman – a pioneer of the biomolecular computing; the ph...Figure 1.6 The principle of Leonard Adleman's DNA computer to solve the “tra...Figure 1.7 The DNA computer playing the tic‐tac‐toe game. Shown in the foreg...Figure 1.8 Atomic force microscopy (AFM) images of DNA origami with differen...Figure 1.9 An example of a DNA chip used in the DNA sensing and computing. T...Figure 1.10 Logic program (a) and automatically generated chemical reaction ...Figure 1.11 PCR method for copying DNA molecules: a thermal cycler, componen...Figure 1.12 Apparatus operating as the end‐to‐end automatic DNA data storage...
2 Chapter 2Figure 2.1 Adleman's DNA computing procedure [2]. For (a) given super graph,...Figure 2.2 Lipton's graph [3] for constructing a binary number for a general...Figure 2.3 Representation of surface‐based DNA computing method [4].Figure 2.4 Representation of surface‐bound DNA sequence.Figure 2.5 Illustration of four literal strings for the DNA hairpin formatio...Figure 2.6 (a) The five‐node graph and (b) its complementary graph used to s...Figure 2.7 Chao's single‐molecule DNA navigator [13] for solving the maze.Figure 2.8 DNA origami is a group of linked dsDNA. The structure consists of...
3 Chapter 3Figure 3.1 The simulation of a register machine. (a) Simulation of bounded r...Figure 3.2 State graph with state transition implemented by CRNs.Figure 3.3 Implementation of Rule 110 Automata. Two different arrangements ...Figure 3.4 Diagrams of the DNA implementation models. (a) Mapping model of b...Figure 3.5 The system performing encoding, computing, and decoding signals i...Figure 3.6 (a) Sequence of reactions for the three‐phase clock based on the ...Figure 3.7 A folded eight‐point four‐parallel real‐valued FFT processor.Figure 3.8 Molecular reactions for each element of the FFT processor in Figu...
4 Chapter 4Figure 4.1 Examples of deoxyribozyme‐based logic gates. (a) One of the first...Figure 4.2 AND deoxyribozyme ligase gate connected to YES RCDZ gates. (a) DN...Figure 4.3 Design of strand displacement (seesaw) DNA logic gates [53]. (a)