Molecular Computing - page 82



NAG (N-acetylglucosamine), in linear recognition, 43

Negative image enhancement, 119

Negative (molecular) recognition, 35

Neural networks. See also Belousov-Zhabotinsky system

chemically implemented, example of, 136-138

with lateral connections, 103-104

shunting on-center off-surround feedback networks, analogy with reaction-diffusion systems, 106

with sigmoidal feedback, signal processing of, 104-105

Neutral molecules, in molecular recognition, 40-41

Nonlinear chemical medium, in reaction-diffusion system, 64. See also Belousov-Zhabotinsky system

Nonstirred reagent layer, 66

NP-complete. See Hamiltonian Path Problem; Maximal clique problem



One-dimensional breather machines. See Cellular automata, one-dimensional; DNA, breather waves in

Optical memories. See 3D (optical) memories

Organic synthesis used in nanoscale engineering, 197-198



Quantum effects in molecular devices, 196-197

effects on reliability, 199-200

Palladium processor, as example of chemical computer doing image processing, 68-69

logical gates implemented with, 75-76

Particle guns, 81

PCR. See Polymerase chain reaction

Percolation thresholds, using reaction-diffusion to investigate, 141

Phase waves, velocity of, 125

Photonic molecular devices, 49-51

Plane subdivision, using chemical processor for, 67-68

Pocket, in molecular recognition, 35

Polymerase chain reaction (PCR), 160, 161, 162

sources of error in, 178

used in construction of site-specific mutations, 212-213

Polymer matrices

use of in encapsulating enzymes in biosensors, 228-229

use of in reaction-diffusion systems, 142-144

Positive image enhancement, 119

Positive (molecular) recognition, 35

Prairie fire transformation, 111. See also Grass-fire transformation

Problem size, xiv, 94-95

Programmed chain reaction, 168-171

Programmed mutagenesis. See DNA computing, algorithms



Reaction-diffusion processors

cells of, as primitive processors, 102-103

definition of, 64

Reaction-diffusion paradigm, as possible explanation of human behavior, 85-87

as example of non-von Neumann system, 92

Reaction-diffusion systems. See also Belousov-Zhabotinsky reaction

arsenic-iodide system, 136

chlorite-iodine system, 134-138

equivalence to neural networks, 104, 106, 107

human brain, analogy with, 147-148

simulations of, 138-141

Receptor, definition of, 34

Reliability of molecular electronics, estimation of, 199-201

Respiration process, energy liberation in, 221-222

River quality monitoring using microbial sensors, 241

RNA editing, in cells, 181-182

Robots, reaction-diffusion system used as unconventional controller for, 70-72

artificial cilia, 72-73

coupling with nonstandard actuators, 71-72

light-seeking, explanation of using diffusion waves as controller for, 71



Saccharide sensors. See Biosensors, saccharide sensors

Satellite pictures, image processing of, 119

Scheibe aggregates, 80

Scroll waves, 145

Segmentation of image, 116

Self-assembly, 52-56

of self-sorting helicates, 54-55

Self-organization, in molecular systems, 52

Self-replication in molecular systems, 58

Sequential one-photon memory. See 3D (optical) memories, sequential one-photon

Shortest path in a labyrinth, using Belousov-Zhabotinsky reaction to determine, 121-133

Signal amplification, in chiral system, 54

Simulations, of reaction-diffusion systems, 85-87, 138-141

Simultaneous two-photon memory. See 3D (optical) memories, simultaneous two photon

Single-molecular bit, possibility of, 200-201

Skeletonization of image using chemical computers, 68-70, 116

Spherical recognition, molecular, 38-39

size discrimination in, 38

Spiral waves, 145

Spots on the skin of a cat, image restoration of, 120-121

Staggered extension process (StEP) in DNA manipulation, 217

Static results from a Belousov-Zhabotinsky reaction, using precipitate in skeletonizing, 69

Stationary circuit, examples of chemical-based logical gates

kinetic, 74

waves in excitable media, 75

Stirred-tank reactors. See Continuous-flow stirred tank reactors

Structural complexity. See Complexity, structural

Substrate, definition of, 34

Symport, in membrane transport, 49