Enzyme-Based Computing Systems (eBook)

Evgeny Katz received his Ph.D. in Chemistry from Frumkin Institute of Electrochemistry (Moscow), Russian Academy of Sciences, in 1983. He was a senior researcher in the Institute of Photosynthesis (Pushchino), Russian Academy of Sciences, in 1983-1991. In 1992-1993 he performed research at München Technische Universität (Germany) as a Humboldt fellow. Later, in 1993-2006, Dr. Katz was a Research Associate Professor at the Hebrew University of Jerusalem. Since 2006 he is Milton Kerker Chaired Professor at the Department of Chemistry and Biomolecular Science, Clarkson University, NY (USA). His scientific interests are in the broad areas of bioelectronics, biosensors, biofuel cells, biomolecular information processing and recently in forensic science.

INTRODUCTION - FROM COMPUTING NEEDS TO BIOMOLECULAR SCIENCE
Unconventional Computing Motivations and Needs
Chemical computing: Logic Gates, Arithmetic Devices and Memory Systems
Biomolecular Computing Systems ? Advantages and Problems
Logic Systems Based on DNA, DNAzymes, Aptamers, Oligopeptides and Biological Cells
Enzyme-Based Logic Gates ? General Assumptions and Definitions

SIMPLE BOOLEAN LOGIC GATES BASED ON ENZYME-CATALYZED REACTIONS
YES (Identity) Logic Gate
NOT (Inverted Identity) Logic Gate
OR Logic Gate
NOR Logic Gate
AND Logic Gate
NAND Logic Gate
XOR Logic Gate
Resettable and Reconfigurable Logic Gates

OPTIMIZATION OF ENZYME LOGIC GATES
Theoretical Models
Experimental Work
'Filter' Systems for Improving the Gates Performance

LOGIC NETWORKS

SOPHISTICATED REVERSIBLE LOGIC SYSTEMS
Spatial Separation of Enzyme Logic Operation - The Use of Flow Devices
Controlled NOT (CNOT) Logic Gate
Feynman Gate
Toffoli Gate
Peres Gate
Fredkin Gate

TRANSDUCTION OF SIGNALS GENERATED BY ENZYME LOGIC GATES
Optical Analysis of the Output Signals Generated by Enzyme Logic Gates
Electrochemical Analysis of the Output Signals
Macro/Micro/Nano-Mechanical Transduction of Output Signals

COMPUTING AND ARITHMETIC ELEMENTS BASED ON ENZYME REACTIONS
Multiplexer and Demultiplexer Devices
Half-adder and half-subtractor Devices
Problems and Challenges in Constructing Full-adder and Full-subtractor Devices Based on Enzyme Reactions

ENZYME-BASED MEMORY SYSTEMS
Write-Read-Erase Systems Based on Enzyme reactions
Set-Reset Flip-Flop Based on Enzyme reactions
Toggle (T) Flip-Flop Based on Enzyme reactions
Delay (D) Flip-Flop Based on Enzyme reactions
Memristor Device Based on Enzyme reactions
Associative Memory Based on Enzyme reactions

DIGITAL (BINARY) BIOSENSORS BASED ON ENZYME LOGIC GATES
General Definitions and Possible Applications
Enzyme-Logic Systems for Processing Biological Biomarkers

INTERFACING OF ENZYME-LOGIC SYSTEMS WITH VARIOUS BIOELECTRONIC DEVICES
Signal-Processing and Controlling of Biomolecular Release Systems
Signal-Processing and Controlling of Biofuel Cells

INTERFACING ENZYME-LOGIC GATES WITH DNA COMPUTING SYSTEMS - INTEGRATED BIOMOLECULAR COMPUTING

CONCLUSIONS AND PERSPECTIVES
Is a Biomolecular Computer Possible?
Other Applications
Short and Long Perspectives and Challenges