Index_D

D

Data encryption standard (DES). See DNA computation, algorithms

Detecting bisector point between two points of a plane, 67

Deterministic computer, definition of, 2

Diffusion length, diffusion coefficient in reaction-diffusion systems, 103

Directed evolution, 216-217

Discrete Voronoi diagram, 67-68

DNA

breather waves in, 77-80

excitons as equivalents of, 80-81

gates in, 77-80

using blocks of as cellular automata, 171-172

DNA computing, 244

advantages of, 157

algorithms and problems (see also Gene scrambling; RNA editing; Cell computation)

3SAT problem, 167

solving in a cell, 184

addition of two non-negative numbers, 168-171

Boolean circuit, finding all inputs, 163-165

Borromean rings for computation, 172

cellular automata in, 171-172

data encryption standard (DES), 175-176

dynamic programming problems, 176

generate-and-test algorithms, 163-167

graph connectivity problem, 176

Hamiltonian Path Problem, 153-156, 180, 181-182

Knight's problem, 166-167

matrix multiplication, 174-175

maximal clique problem, 165

programmed chain reactions (algorithms) 168-175

programmed mutagenesis, 172-173

sources of error (see sources of error)

sticker representation, 165-166

time necessary, 156

whiplash PCR, 173-174

comparison with silicon, 167

sources of error, 177-180

DNA ligation, enhanced, 46, 47

DNA manipulation, 172-173

RNA editing being similar, 182

tools used and definitions, 158-161, 212-215

amplify, 161

anneal, 159

append, 161

cassette mutagenesis, 212-213, 214

cut, 159

destroy, 159

ligate, 159

mark, 161

melt, 159

merge, 160

mismatched primer mutagenesis, 213, 215

polymerase extension, 159

programmed mutagenesis, 172-173, 182

reverse chirality, 160, 174

separate by length, 160

separate by subsequence, 161

staggered extension process (StEP) 217

unmark, 161

Dynamic complexity. See Behavioral complexity