Molecular Computing - page 70


Index

3CNF-SAT or 3SAT, solving in a cell, 184

3D (optical) memories

branched photocycle (see sequential one-photon)

comparison of bit density with other technology, 195

holographic, 203-204

multiplexing, techniques and necessity for, 211

simultaneous two-photon, 205

sequential one-photon, 205-208

erasure process, 207, 208

error analysis, 211

global erasure in prototype system, 209

reading process, 206, 207, 208

wavelengths used in data storage, 206

writing process, 206, 207-208

writing process in prototype system, 209

A

Acetylcholine sensor. See Biosensors, acetylcholine sensor

Actuators, gel, triggered by Belousov-Zhabotinsky reaction, 72, 73

Adaptation in proteins, 8

Adaptation of system to physical dynamics (artificial evolution), 26

Adenine, binding of in a cleft, 41

Adenosine mono, di, and triphosphate (AMP, ADP, ATP) in molecular recognition, 41, 45-46, 51

ATP use in respiration process, 221-222

Aerial and satellite pictures, image processing of, 119

Alcohol sensor. See Biosensors, alcohol sensor

Algorithmic complexity. See Complexity, algorithmic

Allostery, 36

definition of, 44

Amino acid sensor. See Biosensor, amino acid sensor

Ammonium ion (NH4), 40, 41

effects of binding on pKa, 43

AND gates. See Wave gates, AND

Anion recognition, 41-42

Antenna, in photoluminescence, examples of, 50

Antibiotic resistance, increased, 177

Antiport, in membrane transport, 49

Ant paradigm, 85-86

Architectures

compressible, 1, 3-4, 5-6

general purpose, 4

new meaning in biological computers, 8

neuromolecular, 27-28

nonprogrammable, 3-4, 6-8

structurally programmable, 5 (see also compressible)

Arsenic-iodine reaction, used as a coupled reaction-diffusion system, 136

Associative memories, definition of, 203. See also Bacteriorhodopsin, holographic associative memories

ATP. See Adenosine

Autocatalysis. See Self-replication



Index

B

Bacteriorhodopsin

associative memories (see holographic associative memories; 3D [optical] memories)

comparison of size with present semiconductor elements, 193-194

energy storage use in Halobacterium salinarium, 191, 201

holographic associative memories, 203-204 (see also 3D [optical] memories)

data searches, 203

entering images, 203

holographic properties, 201

photonic properties, 201-203

stability of different states of, 202-203

Behavior, complexity of. See Complexity, behavioral

Belousov-Zhabotinsky reaction (system)

color changes in, 115-116

history of discovery, 108

how a Belousov-Zhabotinsky reaction works, 68-69, 109

pictures of temporal evolution in

basic periodic process in, 110

black-and-white image processing in, 114

changes depending on different starting conditions, 111

enhancement of picture fragments in, 119

extraction of original image from low-quality data, example of, 121

half-tone pictures in, 117, 118

image processing mechanism in, 115, 116

labyrinths, 123, 127, 128, 129, 132

neural networks, similarity to processing in, 98

restoration of individual components in, 120

trigger waves in, 97, 108

trigger waves vs. circular waves, 97

wave-based logical circuit in, 74-75

as system of parallel processors, 66

Binding (vs. recognition), in catalytic cycles, 45

Biocomputers, definition of, 243

Bioelectronics. See also Molecular devices

comparison with semiconductor electronics, advantages of, 192-193

control and power supply for bioelectronics, 101

Biomolecular systems and biomolecular computing

basic principles of, 100-101

genetic engineering, used to improve materials, 212, 217

input of information into, 12-13, 100

output of results, 101

definition of, 92

Biosensors

acetylcholine sensor, 234

alcohol sensor, 230-231

based on microbial yeast, 241

amino acid sensor, 231

ATP sensor, 234

biochemical oxygen demand (BOD) sensor, 241

chemiluminescence-based, 234-235

enzyme-based, 229-235

fish-freshness sensor, 232-233

glucose sensor

commercialization of, 227, 229

enzyme based, 229, 234

general structure of, 224-225

lifetime of, 255

reaction response, 225-226

history of, 226

immunosensor, 236-239

steric hindrance in, 237

QCM based, 236-237

using a surface plasmon resonance (SPR) device, 239

ISFET-based, 233-234

microbial sensors, 239-241

respiration-type, 240

alcohol sensor based on microbial yeast, 241

biochemical oxygen demand (BOD) sensor, 241

microfabrication of, 227, 229, 233-234

molecular recognition material in biosensor membrane, techniques of immobilization, 226-228

nucleic acid sensors, 231-232

adenosine, 231

guanine, 231

inosine, 231

xanthine, 231

saccharide sensors, 229-230

structure of, 226-227

thermistor-using sensor, 234

transducer

definition of, 225

examples of, 226

tributylene sensor, 234

urea sensor, 232, 234

Bit of information storage vs. area required, trend in years, 195

Blocked cellular automata, 171-172

BOD sensor. See Biosensors, biochemical oxygen demand (BOD) sensor, 241

Boolean circuit, embedded, 73-76

Borromean rings, 172

Brain, organization of, 92

Branched photocycle memory architecture. See 3D (optical) memories, sequential one-photon

Branching points, 129-130, 132

Breathers. See Collision-based computing, breathers in DNA molecules as example of

Brownian motion. See Brownian search

Brownian search, 7