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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) ...Figure 4.4 DNA strand displacement logic gates attached to a DNA origami til...Figure 4.5 Design of molecular beacon (MB)‐based DNA logic gates. (a) MB pro...Figure 4.6 4WJ DNA logic gates and tile‐integrated DNA circuits. (a) 4WJ NOT...

5 Chapter 5Figure 5.1 Nucleic acid nanostructure designing techniques. (a) DNA origami ...Figure 5.2 (a) Examples of the diverse application of nucleic acid aptamers....Figure 5.3 Common binary logic gate symbols and truth tables.Figure 5.4 Logic gates design principle using MG‐binding RNA aptamer. (a) Re...Figure 5.5 Examples of combinatorial logic gates using half‐adder and full‐a...

6 Chapter 6Figure 6.1 Representative tile‐based DNA nanostructures. (a) 2D DNA crystall...Figure 6.2 Representative DNA origami nanostructures. (a) DNA origami folded...Figure 6.3 DNA/RNA nanotechnology‐enabled toolbox for synthetic circuits. A ...Figure 6.4 Typical AND gate circuits. (a) A DNAzyme‐enabled AND gate.. (...Figure 6.5 Scheme of an integrated live‐cell circuit enabled by DNA/RNA nano...

7 Chapter 7Figure 7.1 Engineering steps of DNA switches. (I) DNA can adopt a wide range...Figure 7.2 (a) Cartoon representation of the population‐shift mechanism. The...Figure 7.3 Based on the population‐shift model, different strategies exist t...Figure 7.4 Creating switches based on the population‐shift model for double ...Figure 7.5 Exploiting allosteric effectors to create logic gates. (a) Using ...Figure 7.6 Examples of logic gate created using the strategies discussed in ...Figure 7.7 (a) Two or more switches with different affinities for the input ...

8 Chapter 8Figure 8.1 The universal input/output mechanism of DNA‐based logic circuit. ...Figure 8.2 Schematic representation of the YES gate based on the hairpin str...Figure 8.3 Schematic representation of the DNA computing assembly based on t...Figure 8.4 Schematic representation of cascaded DNA computation based on the...Figure 8.5 Schematic representation of the AND gate based on the strand disp...Figure 8.6 Schematic representation of the parity generator/checker based on...Figure 8.7 Schematic representation of the AND logic gate that consists of t...Figure 8.8 Schematic representation of the three‐input majority logic gate....Figure 8.9 Schematic representation of the 2‐to‐4 DC.Figure 8.10 The electronic diagram (i) and the schematic representation (ii)...Figure 8.11 (a) Schematic representation of the label‐free 8‐to‐3 encoder. (...Figure 8.12 (i) Schematic representation of DNA structural conversions induc...Figure 8.13 Schematic representation of the logic operations based on HP26‐t...Figure 8.14 (i) Schematic representation of the DNA‐MTC supramolecular logic...Figure 8.15 Schematic representation of the reconfigurable DNA‐supramolecula...

9 Chapter 9Figure 9.1 Truth tables and symbols for the elementary two‐input Boolean log...Figure 9.2 Three‐color QD logic gates. (I) Mechanism for control of hybridiz...Figure 9.3 Time‐gated photonic logic gates with LLCs as FRET donors. (I) ET‐...Figure 9.4 DNA‐mediated AuNP aggregation as a colorimetric indicator. (I) Vi...Figure 9.5 Three‐input logic gate with an AuNP quencher. (I) Cooperative bin...Figure 9.6 PAA‐templated fluorescent AgNC logic gates. (I) Transfer of AgNC ...Figure 9.7 Fluorescence quenching by graphene oxide for two‐output logic cir...Figure 9.8 Logic gate with CDs (labeled as “C‐dots”) and EB. (I) Adsorption ...Figure 9.9 Three‐input logic circuit with a conjugated polymer FRET donor. (...

10 Chapter 10Figure 10.1 Principle of DNA strand displacement (DSD) reactions (a,b) and o...Figure 10.2 Mechanism of the genelet reaction system (a) and network oscilla...Figure 10.3 Mechanism of the PEN DNA toolbox reaction system (a) and network...Figure 10.4 Reaction–diffusion edge detection pattern engineered with DNA st...Figure 10.5 PEN autocatalyzers generate programmable concentration fronts th...Figure 10.6 “Go‐fetch” fronts (a) and waves and spirals with PEN reactions (...Figure 10.7 Strategies to control the diffusion and geometry of RD patterns....Figure 10.8 Steady‐state “colony” formation in a population of synergic part...Figure 10.9 Illustration of Wolpert's concept of positional information as a...Figure 10.10 Static pattern of positional information engineered with DNA st...Figure 10.11 Static patterns of positional information can be engineered wit...

11 Chapter 12Figure 12.1 (a) The operation of half‐adder/half‐subtractor based on the uni...Figure 12.2 (A) The operation of encoder/decoder based on the universal GO/D...Figure 12.3 (a) The parity checker for identifying even/odd numbers from nat...Figure 12.4 (a) The five‐digit DNA keypad lock based on silver microspheres ...Figure 12.5 Concatenated DNA logic circuits with (a) visual.(b) fluoresc...Figure 12.6 (a) Schematic illustration of the DNA “contrary logic pairs” lib...Figure 12.7 The integration of DNA computing with (A) peptides. (a) Equivale...

12 Chapter 13Figure 13.1 Toehold‐mediated strand displacement reactions. (a) A DNA duplex...Figure 13.2 Toehold switch riboregulators [18] and input logic [20]. (a) Toe...Figure 13.3 Switching guide RNAs using toehold‐mediated strand displacement....Figure 13.4 Activation of RNA interference via toehold‐mediated strand displ...

13 Chapter 14Figure 14.1 A prototypical DNA strand displacement reaction showing one of t...Figure 14.2 Allosteric toehold mechanism. A first input invades the target d...Figure 14.3 (a) Cooperative hybridization of the inputs induces the displace...Figure 14.4 Associative toehold mechanism. The helper strand (orange) facili...Figure 14.5 Remote toehold mechanism. A spacer separates the toehold and the...Figure 14.6 The toehold exchange reaction. The process is fully reversible v...Figure 14.7 Programmed reconfiguration of DNA assemblies using the strand di...Figure 14.8 Programmed reconfiguration of DNA assemblies using the strand di...Figure 14.9 Dynamic reconfiguration of DNA‐based interlocked catenanes using...Figure 14.10 Programmed motion of a bipedal DNA walker. An attaching strand ...Figure 14.11 Autonomous directional motion of a DNA bipedal walking device. ...Figure 14.12 A DNA‐based transporter. (a) Details of the movement of the wal...Figure 14.13 Directed graph G representing Adleman's Hamiltonian path proble...Figure 14.14 Adleman's DNA solution to the Hamiltonian path problem.Figure 14.15 Graphical representation of a 2‐SAT problem.Figure 14.16 The Boolean logic operators NOT (a), AND (b), and OR (b). The d...Figure 14.17 (a) Deoxyribozyme‐based AND logic gate design with hairpins pre...Figure 14.18 Strand displacement cascade illustrating a toehold exchange str...Figure 14.19 The DNA seesaw architecture. (a) Abstract seesaw gate formalism...Figure 14.20 Operation of logic gates immobilized on a solid‐phase support. ...Figure 14.21 Early developments in DNA catalytic systems. (a) Kinetic contro...Figure 14.22 Entropy‐driven catalytic DNA system. The catalyst first interac...

14 Chapter 15Figure 15.1 Basic molecular logic units and their activation during training...Figure 15.2 The molecular assembly line and its operation. (a) The basic com...Figure 15.3 Scheme of a walking DNAzyme and its track. (a) The walking princ...Figure 15.4 Domain‐level (a) and schematic (b) representations of the miRNA‐...Figure 15.5 Mean squared displacement, 〈x²(t)〉.Figure 15.6 The irreversible catalysis of substrates to products leads to th...Figure 15.7 (a) Implementation of a state transition through DNAzymes. (b)

15 Chapter 16Figure 16.1 Conjectured self‐assembly of DNA origami. (a) Phase 1: Synthesis...Figure 16.2 Simplistic illustration of primitives: a conceptual illustration...Figure 16.3 Strand displacement reaction. (a) Before strand displacement. (b...Figure 16.4 Zip transformation. (a) Before zip. (b) After zip. Strands s1, …...Figure 16.5 Unzip transformation. (a) Before unzip. (b) After unzip. Strands...Figure 16.6 Zip and unzip by DNA hairpins. (a) A pair of adjacent hairpins. ...Figure 16.7 Zip and unzip by strand‐displacing polymerase. (a) Unhybridized ...Figure 16.8 AFM characterization. (a) M1 before zip. (b) M1 after zip. (c) M...Figure 16.9 Dynamic devices created from a single DNA origami. (a) Examples ...Figure 16.10 Dynamic network of nanocontainers using DNA origami transformer...Figure 16.11 Initiated transformations: repeated units of these consolidated...

16 Chapter 17Figure 17.1 Conventional DNA computing and its decoding. (A) Adleman [1] des...Figure 17.2 Applications of nanopore technology. (a) Schematic illustration ...Figure 17.3 Nanopore decoder methodology. NAND operation in a droplet system...Figure 17.4 DNA relay mechanism. (a–f) Conceptual diagrams of the DNA relay ...Figure 17.5 Nanopore decoder applications. (a) Four individual operations as...Figure 17.6 Nanopore detection of miRNAs. (a) MiRNA detection using DNA prob...

17 Chapter 18Figure 18.1 Pipeline of a typical DNA‐based digital storage system.

18 Chapter 19Figure 19.1 General scheme of the system operation: the enzyme computing sys...Figure 19.2 Two enzyme systems used in this study and their corresponding lo...Figure 19.3 (a) Potential measurements on the sensing electrode – general sc...Figure 19.4 (a) Optical analysis of the DNA released (note that the DNA was ...Figure 19.5 The general scheme illustrating the DNA‐based 3‐AND logic gate o...Figure 19.6 Principal scheme of a three‐input deoxyribozyme AND gate. Strand...Figure 19.7 Digital performance of the DNA logic gate. (a) General scheme. (...Figure 19.8 The truth table (a), block diagram (b), and equivalent electroni...Figure 19.9 Experimental realization of the biocatalytic Fredkin gate in the...Figure 19.10 Experimental realization of the Fredkin gate (photo of the flow...Figure 19.11 The block scheme of the entire system including (A) the enzyme‐...Figure 19.12 Operation of the electrochemical interface between the enzyme a...Figure 19.13 (A) Logic scheme (including the ID and XOR gates operating in ...Figure 19.14 Schematic representation of the DNA reactions mimicking XOR fun...Figure 19.15 (a) Nerve cells deposited on a microelectrode array. (b) Beyond...