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Enzyme-Based Computing Systems

Author: Evgeny Katz
Publisher: Weinheim, Germany : Wiley, [2019]
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:
This systematic and comprehensive overview of enzyme-based biocomputing is an excellent resource for scientists and engineers working on the design, study and applications of enzyme-logic systems.
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Genre/Form: Electronic books
Additional Physical Format: Print version:
Katz, Evgeny.
Enzyme-Based Computing Systems.
Newark : John Wiley & Sons, Incorporated, ©2019
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Evgeny Katz
ISBN: 9783527819997 3527819991 9783527819966 3527819967
OCLC Number: 1105958596
Notes: Chapter 12 Release of Molecular Species Stimulated by Logically Processed Biomolecule Signals.
Description: 1 online resource (422 pages)
Contents: Cover --
Title Page --
Copyright --
Contents --
Preface --
Acknowledgment --
List of Abbreviations --
Chapter 1 Introduction --
1.1 Motivation and Applications --
1.2 Enzyme-Based Logic Gates and Short Logic Circuits --
References --
Chapter 2 Boolean Logic Gates Realized with Enzyme-Catalyzed Reactions: Unusual Look at Usual Chemical Reactions --
2.1 General Introduction and Definitions --
2.2 Fundamental Boolean Logic Operations Mimicked with Enzyme-Catalyzed Reactions --
2.2.1 Identity (YES) Gate --
2.2.2 Inverted Identity (NOT) Gate --
2.2.3 OR Gate --
2.2.4 NOR Gate --
2.2.5 XOR Gate --
2.2.6 NXOR Gate --
2.2.7 AND Gate --
2.2.8 NAND Gate --
2.2.9 INHIB Gate --
2.2.10 Summary on the Basic Boolean Gates Realized with Enzyme Systems --
2.3 Modular Design of NOR and NAND Logic Gates --
2.4 Majority and Minority Logic Gates --
2.5 Reconfigurable Logic Gates --
2.5.1 3-Input Logic Gates Switchable Between AND-OR Logic Functions Operating in a Solution --
2.5.2 Enzyme-Based Logic Gates Switchable Between OR, NXOR, and NAND Boolean Operations Realized in a Flow System --
2.6 Conclusions and Perspectives --
References --
Chapter 3 Optimization of Enzyme-Based Logic Gates for Reducing Noise in the Signal Transduction Process --
3.1 Introduction --
3.2 Signal Transduction Function in the Enzyme-Based Logic Systems: Filters Producing Sigmoid Response Functions --
3.2.1 Identity (YES) Logic Gate Optimization --
3.2.2 AND Logic Gate Optimization --
3.2.3 OR Logic Gate Optimization --
3.2.4 XOR Logic Gate Optimization --
3.3 Summary --
References --
Chapter 4 Enzyme-Based Short Logic Networks Composed of Concatenated Logic Gates --
4.1 Introduction: Problems in Assembling of Multistep Logic Networks --
4.2 Logic Network Composed of Concatenated Gates: An Example System --
4.3 Logic Networks with Suppressed Noise in the Presence of Filter Systems. 4.4 Logic Circuits Activated with Biomolecular Signals and Magnetic Field Applied --
4.4.1 Biocatalytic Reactions Proceeding with Bulk Diffusion of Intermediate Substrates/Products and with Their Channeling --
4.4.2 Magneto-Controlled Biocatalytic Cascade Switchable Between Substrate Diffusion and Substrate Channeling Modes of Operation --
4.4.3 Logic Signal Processing with the Switchable Biocatalytic System --
4.5 The Summary: Step Forward from Single Logic Gates to Complex Logic Circuits --
References --
Chapter 5 Sophisticated Reversible Logic Systems --
5.1 Introduction --
5.1.1 Reversible Logic Gates and Their Features --
5.1.2 Logic Reversibility vs. Physical Reversibility --
5.1.3 Integration of Reversible Logic Gates into Biomolecular Computing Systems --
5.1.4 Spatial Separation of Enzyme Logic Operation: The Use of Flow Devices --
5.2 Feynman Gate: Controlled NOT (CNOT) Gate --
5.3 Double Feynman Gate (DFG) Operation --
5.4 Toffoli Gate Operation --
5.5 Peres Gate Operation --
5.6 Gates Redirecting Output Signals --
5.6.1 Controlled-Switch Gate --
5.6.2 Fredkin (Controlled-Swap) Gate --
5.7 Advantages and Disadvantages of the Developed Approach --
5.7.1 Advantages --
5.7.2 Disadvantages --
5.8 Conclusions and Perspectives --
References --
Chapter 6 Transduction of Signals Generated by Enzyme Logic Gates --
6.1 Optical Analysis of Output Signals Generated by Enzyme-Based Logic Systems --
6.1.1 Optical Absorbance Measurements for Transduction of Output Signals Produced by Enzyme-Based Logic Gates --
6.1.2 Bioluminescence Measurements for Transduction of Output Signals Produced by Enzyme-Based Logic Gates --
6.1.3 Surface Plasmon Resonance (SPR) Measurements for Transduction of Output Signals Produced by Enzyme-Based Logic Gates --
6.2 Electrochemical Analysis of Output Signals Generated by Enzyme-Based Logic Systems. 6.2.1 Chronoamperometric Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems --
6.2.2 Potentiometric Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems --
6.2.3 pH Measurements as a Tool for Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems --
6.2.4 Indirect Electrochemical Analysis of Output Signals Generated by Enzyme-Based Logic Systems Using Electrodes Functionalized with pH-Switchable Polymers --
6.2.5 Conductivity Measurements as a Tool for Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems --
6.2.6 Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems Using Semiconductor Devices --
6.3 Macro/Micro/Nano-mechanical Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems --
6.3.1 Mechanical Bending of a Cantilever Used for Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems --
6.3.2 Quartz Crystal Microbalance (QCM) Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems --
6.3.3 Atomic Force Microscopy (AFM) Transduction of Chemical Output Signals Produced by Enzyme-Based Logic Systems --
6.4 Conclusions and Perspectives --
References --
Chapter 7 Circuit Elements Based on Enzyme Systems --
7.1 Enzyme-Based Multiplexer and Demultiplexer --
7.1.1 General Definition of the Multiplexer and Demultiplexer Functions --
7.1.2 2-to-1 Digital Multiplexer Based on the Enzyme-Catalyzed Reactions --
7.1.3 1-to-2 Digital Demultiplexer Based on the Enzyme-Catalyzed Reactions --
7.1.4 1-to-2 Digital Demultiplexer Interfaced with an Electrochemical Actuator --
7.2 Biomolecular Signal Amplifier Based on Enzyme-Catalyzed Reactions --
7.3 Biomolecular Signal Converter Based on Enzyme-Catalyzed Reactions. 7.4 Utilization of a Fluidic Infrastructure for the Realization of Enzyme-Based Boolean Logic Circuits --
7.5 Other Circuit Elements Required for the Networking of Enzyme Logic Systems and General Conclusions --
References --
Chapter 8 Enzyme-Based Memory Systems --
8.1 Introduction --
8.2 Enzyme-Based Flip-Flop Memory Elements --
8.2.1 Set/Reset (SR) Flip-Flop Memory Based on Enzyme-Catalyzed Reactions --
8.2.2 Delay (D) Flip-Flop Memory Based on Enzyme-Catalyzed Reactions --
8.2.3 Toggle (T) Flip-Flop Memory Based on Enzyme-Catalyzed Reactions --
8.2.4 Enzyme-Based Flip-Flop Memory Systems: Conclusions and Perspectives --
8.3 Memristor Based on Enzyme Biocatalytic Reactions --
8.3.1 Memristors: From Semiconductor Devices to Soft Matter and Biomolecular Materials --
8.3.2 The Memristor Device Based on a Biofuel Cell --
8.3.3 The Memristor Device Controlled by Logically Processed Biomolecular Signals --
8.3.4 Enzyme-Based Memristors: Conclusions and Perspectives --
8.4 Enzyme-Based Associative Memory Systems --
8.4.1 Associative Memory: Biological Origin and Function --
8.4.2 Realization of the Associative Memory with a Multienzyme Biocatalytic Cascade --
8.4.3 Enzyme-Based Associative Memory: Challenges and Perspectives --
8.5 Enzyme-Based Memory Systems: Challenges, Perspectives, and Limitations --
References --
Chapter 9 Arithmetic Functions Realized with Enzyme-Catalyzed Reactions --
9.1 Molecular and Biomolecular Arithmetic Systems: Introduction and Motivation --
9.2 Half-Adder --
9.3 Half-Subtractor --
9.4 Conclusions and Perspectives --
References --
Chapter 10 Information Security Applications Based on Enzyme Logic Systems --
10.1 Keypad Lock Devices as Examples of Electronic Information Security Systems --
10.2 Keypad Lock Systems Based on Biocatalytic Cascades --
10.3 Other Biomolecular Information Security Systems. 10.3.1 Steganography and Encryption Methods Based on Bioaffinity Complex Formation Followed by a Biocatalytic Reaction --
10.3.2 Barcodes Produced by Bioelectrocatalytic Reactions --
10.4 Summary --
References --
Chapter 11 Enzyme Logic Digital Biosensors for Biomedical, Forensic, and Security Applications --
11.1 Introduction: Short Overview --
11.2 From Traditional Analog Biosensors to Novel Binary Biosensors Based on the Biocomputing Concept --
11.3 How Binary Operating Biosensors Can Benefit Biomedical Analysis: Requirements, Challenges, and First Applications --
11.4 Binary (YES/NO) Analysis of Liver Injury Biomarkers: From Test Tube Probes to Animal Research --
11.5 Further Examples of Injury Biomarker Analysis Using AND/NAND Logic Gates --
11.5.1 Soft Tissue Injury (STI) Logic Analysis --
11.5.2 Traumatic Brain Injury (TBI) Logic Analysis --
11.5.3 Abdominal Trauma (ABT) Logic Analysis --
11.5.4 Hemorrhagic Shock (HS) Logic Analysis --
11.5.5 Oxidative Stress (OS) Logic Analysis --
11.5.6 Radiation Injury (RI) Logic Analysis --
11.6 Multienzyme Logic Network Architectures for Assessing Injuries: Aiming at the Increased Complexity of the Biocomputing-Bioanalytic Systems --
11.6.1 The System Structure Based on the Complex Biocatalytic Cascade --
11.6.2 STI Operation Mode of the Logic Network --
11.6.3 TBI Operation Mode of the Logic Network --
11.6.4 Switching Between the STI and TBI Modes and General Comments on the System --
11.7 New Approach in Forensic Analysis: Biomolecular Computing-Based Analysis of Forensic Biomarkers --
11.8 Logic Analysis of Security Threats (Explosives and Nerve Agents) Based on Biocatalytic Cascades --
11.9 Integration of Biocatalytic Cascades with Microelectronics and Wearable Sensors --
11.10 Conclusions and Perspectives --
References.
Responsibility: Evgeny Katz.

Abstract:

This systematic and comprehensive overview of enzyme-based biocomputing is an excellent resource for scientists and engineers working on the design, study and applications of enzyme-logic systems.

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