REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 10 (1997)

The numbers following each term refer to the pages on which it is mentioned. Computer programs are denoted in boldface; databases and journals are in italics. (This document does not contain the minor corrections that were made to the proofs.)

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Absolute rate theory, 115
Accumulation point, 239
Actions, 130
Activation energy, 115
Activator species, 206
Adams-Bashforth algorithm, 205
Advisory Board for the Research Councils (ABRC), 309
Alkanes, 291
Alleles, 28
Allinger, N. L., viii
Alpha-Branch and Bound method, 61
Alternate selection strategies, 24
Alternative crossover schemes, 25
AMBER
, 45
American Theory Conference, 303
Amino acid sequence, 45
Annealed dynamics, 63
Apamin, 44
Aperiodic motion, 238, 262
Area-preserving mapping, 141
Arnold diffusion, 167
Arnol'd tongues, 251, 252
Array processors, 310
Arrhenius equation, 115
Artificial selection, 9
Asymmetric crossover, 54
Asymptotic state, 232, 236
Atlas, 277, 287, 289, 290, 295, 310
Atlas Computer Laboratory, 285, 286, 292, 295
ATMOL
, 285, 289, 296, 297, 303, 306
Atom layer table, 82
Atomic Energy Research Establishment, 286
Atomic Weapons Research Establishment, 304
Attractive fixed point, 145
Attractive manifold, 145
Attractive periodic orbit, 145
Attractors, 199, 236
Augmented phase space, 204
AUTO
, 205
Autocatalysis, 183, 206, 209, 216, 222, 223, 225
Autocode, 276
Avian pancreatic polypeptide inhibitor (APPI), 44

Backbone conformation, 40
Backward Euler method, 200
Ball-and-stick models, 281
Barnett-Coulson expansion, 283
Barrier recrossing, 102
Bartlett, R., 303
Basin of attraction, 236
Basis functions, 52
Belousov-Zhabotinskii (BZ) reaction, 228, 259
Benzene, 37
Biased D-optimal design, 85
Biased designs, 91
Biased diversity, 83
Bifurcation diagram, 193
Bifurcation point, 193, 239
Bifurcations, 133, 185 190
Bimolecular exchange, 119, 120
Bimolecular reactions, 152, 156
Binary chromosomes, 6, 8, 57
Bioactive conformation, 50
Bioinformatics, 310
Biology, 181
Biosynthesis of proteins, 179
Bistability, 182, 183, 186, 188
Bit strings, 80
Blending, 54
BLoop
, 45
Born-Oppenheimer approximation, 102, 108, 128
Bottleneck separatrix, 163
Boulder Conference, 282
Boys, S. F., 278, 292
Breeding, 4
Broken torus, 253
Brownian dynamics, 63
Brusselator, 195, 198, 211
Buckingham, A. D., 290
Building blocks, 17, 25, 30, 38
Butterfly effect, 118

CADPAC
, 311
Cambridge Structural Database
, 95, 298
Cambridge, University of, 277
Canonically conjugate variables, 105
Cantorus, 149, 168
Carbon clusters, 38
Carcinogenic compounds, 307
Cartesian random search, 61
CAVEAT
, 87
CDC computers, 297, 306
Cellular automata, 230
Center Manifold theorem, 133, 150, 163
Central Computing Committee (CCC), 309
Centre Européen Calcul Atomique et Moléculaire (CECAM), 297, 304
CERN, 292, 297
Chaos, 101, 109, 115, 117, 179, 183, 214, 226, 235
Chaotic behavior, 237, 263
Chaotic orbits, 132
Chaotic phase space, 159
Chaotic state, 258
Chaotic systems, 231
Chaotic trajectories, 117, 137, 138, 149, 167, 239
CHARMM
, 50
Chemical Database Service
, 311
Chemical databases, 292, 298
Chemical distance, 50
Chemical diversity, 75, 95
Chemical functionality descriptors, 79, 81, 82, 87, 95
Chemical graphs, 51
Chemical kinetics, 115, 190
Chemical oscillators, 259
Chemical waves, 188, 215
Chemistry, 181
Chemometrics, 37, 79, 282
Chlorite-iodide-malonic acid (CIMA) reaction, 206
Chromosomes, 2, 6, 10, 17, 18, 25, 36, 41, 47
Circle maps, 247, 248, 250, 253, 255
CLARA clustering method, 57
Classical dynamics, 128
Classical Hamiltonian function, 104
Classical mechanics, 103, 117
Classical resonance effects, 120
Clementi, E., 284
CLICHE
, 87
CLOGP
, 79
Closed system, 182, 206
Clustering, 56, 80, 93
Clusters, 37, 38
Collaborative Computational Projects (CCP), 294, 296, 301, 303
Collision-free limit, 103
COLOSSUS, 273
Combinatorial chemistry, 75
Combinatorial explosion problem, 61
Combinatorial library design, 89
Commensurate relationship, 245
Committee for Scientific Policy, 288
Comparative molecular field analysis (CoMFA), 88
Compiler, 276
Computational chemistry, v, 37, 271, 178, 291
Computational crystallography, 289, 292
Computational quantum chemistry, 289, 292
Computational quantum pharmacology, 307
Computational Science Initiative, 310
Computer-aided drug design, 75
Computer-aided instrumentation, 281
Computer-aided synthesis, 281
Computer Board, 272, 288, 300
Computer graphics, v
Computing Review Working Party, 309
Concentration gradients, 205
Configuration interaction (CI), 283, 296, 304, 308
Configuration space, 103
Conformational entropy, 41
Conformational isomerization, 120
Conformational searches, 7, 23, 32, 37, 38, 40, 46, 48
Conjugate gradient, 39
Connectivity indices, 79
Conservation condition, 232
Conservative systems, 129
Constraints, 20
Constructionist approach, 180
Continuation method, 203
Continuous-flow stirred tank reactor (CSTR), 182
Continuum states in atoms and molecules, 301
Convergence, 19
Convergence of journals, vi, viii
Corporate archives, 93
Correlation dimension, 260, 264
Correlation matrix, 83
Correspondence principle, 109
Cottage industry, 312
Coulson, C., 282, 290, 292, 294
Counts, R. W., viii
Coupled Hamiltonian systems, 132
Coupled lattice methods, 230
Coupled map lattices, 231
Coupled ordinary differential equations, 191
Coupled ordinary differential equations lattices, 231
Coupled pair many electron theories (CPMET), 298, 303
Crambin, 45
CRAY computers, 304, 308, 309, 310, 312
CRAY Research Inc., 305
Cross-validated multiple regression, 88
Crossover, 5, 6, 10, 17, 19, 36, 43, 47
Crossover operator, 18, 26, 29, 45, 53
Crossover problems, 21
Crossover rate, 15, 23
Crystal Structure Search and Retrieval (CSSR)
, 298
CSEARCH
, 39, 49, 61, 62
Cubic autocatalysis, 211, 223, 226
Cut-and-splice operator, 31
CYBER 205 computer, 311
Cylindrical manifolds, 120, 153

D-optimal design, 83
Daresbury Laboratory, 292, 301, 302, 309
Darwinian evolution, 4, 27
Database management, 311
Database similarity searching, 80
De Leon-Berne Hamiltonian, 138, 139, 154, 157
De novo design, 63, 89
Defining length, 19
Delay line, 274
Deletion, 54
Density-functional methods, 303
Design matrix, 83
Detailed balance condition, 113
DEUCE computer, 274
Devil's staircase, 250, 251, 257
Dewar, M. J. S., 285
Diatomic molecule, 106
Differential analyzer, 275
Diffusion, 205
Diffusion-induced instability, 206, 208, 212
Digital computers, 273, 279, 304
Dimensionless concentration, 196, 229
Dimensionless variables, 196, 218
Diploid chromosomes, 28
Dirac, P. A. M., 278
Direct CI methods, 298
Directed tweak, 49, 62
Discontinuous transition, 186
Display screen, 275
Dissimilarity, 78
Dissipative systems, 179, 182, 188, 231
Distance constraints, 48, 49
Distance geometry, 49, 62, 63
Distance matrix, 42
Distributed array processor, 305
Diversity score, 90, 97
Diversity sites, 75
Diversity space, 94
DNA, 35, 37, 48, 55
DOCK
, 46
Docking, 46, 63
DOP model, 253, 256, 258, 264
Drug design, vii, 75, 307
Dynamic programming, 56
Dynamical chaos, 118, 119, 129
Dynamical systems, 179

Eckhart Hamiltonian, 290
Ecology, 181
EDSAC computer, 274, 278, 280, 282, 290
EDVAC computer, 278
Ehrenfest theorem, 109
Electrochemical systems, 259
Electron correlation, 294, 306
Electronic Journal of Theoretical Chemistry
, v
Electronic mail (e-mail), 300
Electronic mail groups, 65
Electronic wavefunctions, 102
Electrotopological state index, 81
Elementary particles, 178
Elitism, 11
Elliott 400 series computers, 274
Elliott Committee, 309
Elliptic fixed point, 136, 137, 139, 144
Energy transfer, 103, 126
Engineering Computing Newsletter
, 300
Enzyme-catalyzed reaction, 179
Enzyme kinetics, 191
Epitope effect, 96
Ergodic motion, 131, 139
Evolutionary programming, 47
Evolutionary strategies, 4, 5, 34
Excitable media, 230
Experimental design, 83, 92
Experimental packet-switched system, 300
Explicit method, 201
Extended Mercury Autocode, 276

Factorial design, 77
FAP language, 287
Far from equilibrium, 182
Farey sequence, 247
Features, 52
Feedback, 182, 183, 201, 205, 228
Ferranti computers, 274, 287
Fertilization operator, 29
Fingerprint routines, 80
First-order rate constant, 113
Fisher-Kolmogorov equation, 219
Fitness, 2, 22, 24
Fitness function, 8, 18, 20, 24, 32, 43, 50, 54, 55, 58, 89, 90
Fitness landscape, 2, 13, 48, 58
Fixed point of order, 140
Fixed point of reflection, 145
Fletcher-Reeves method, 290
Floating point operations, 276
Floating Point System 264 (FPS) computer, 310
Floquet exponents, 237, 262
Flowers Report, 285, 288
Flux of trajectories, 156
Focus, 198, 221, 245
Focusing operation, 41
Foliated phase space, 106, 124
Foliated tori, 127, 131, 152
FORTRAN, 287, 289, 306
Forward Euler method, 200
Four-letter alphabet, 35
"Four wise men," 293, 294, 300
Fractal dimension, 260, 264
Fractal object, 236
Fractal torus, 253, 257
Fractional dimension, 236
Frequency factor, 115
Frustrated response, 251
Function evaluations, 21
Fundamental laws, 179
Fundamental particles, 177
Fuzzy logic, 81

GAMESS
, 285, 308
Gametes, 29, 36
Gametogenesis, 36
Gaussian
, 285, 308
Gaussian basis, 279
Gaussian integral evaluations, 289
Gaussian weighted mutations, 35
Gear algorithm, 201, 202
Generational replacement, 25
Generations, 22
Genes, 179
Genesis
, 39
Genetic algorithm (GA), 1, 4, 49, 63, 88, 89
Genetic algorithm codes, 8, 65
Genetic function approximation (GFA), 52
Genome maps, 55
Genotype, 6, 8, 35
Gerratt, J., 294, 303, 307
Global minimum, 1, 2, 15, 20, 42
Global optimization, 1, 21, 44, 58
Global stability, 190
Globally chaotic dynamics, 139
Golden torus, 149
Gordon Research Conference on Computational Chemistry, vii
Government funding, 271
Granularity, 24
Grassberger-Procaccia algorithm, 261
Gray coding, 7, 11, 24
Greedy oversampling, 27
Green's function methods, 298
Green's theorem, 166
Grid search methods, 61, 62
Growing, 46
Guest, M. F., 292, 297, 308

Hamiltonian operator, 105, 106
Hamiltonian systems, 128, 142, 231
Hamilton's equations of motion, 104, 129, 134, 140, 166
Hamming distance, 28
Handy, N. C., 298
Hansch-type analysis, 88
Haploid chromosomes, 28
Harmonic oscillator, 106, 107, 130
Hartree, D. R., 275, 278
Hartree-Fock equations, 275
Hausdorff dimension, 260
HCN, 120, 157
Heaviside step function, 261
HeI2 cluster, 156
Hemoglobin, 280
Henon algorithm, 134, 135
Henon-Heiles Hamiltonian, 132
Heteroclinic fixed point, 146, 147, 148
Heteroclinic orbits, 149
Hierarchical genetic algorithm, 48
Hierarchical potential, 45
High-throughput screening, 75
HINT
, 79
HNSi, 156
Hoffmann, R., viii
Home pages, 65
Homoclinic fixed point, 146, 147
Homoclinic manifold, 162
Homoclinic orbits, 149
Homogeneous systems, 182, 200, 214
HookSpace index, 95
Hop operator, 54
Hopf bifurcation, 195, 198, 212, 234, 244, 245
Hopping, 54
Horse myoglobin, 280
Houk, K. N., viii
Hückel calculation, 276
Hyperbolic fixed points, 137, 139, 145
Hyperbolic manifold, 160
Hypercylinders, 162
Hyperdimensional Poincaré map, 164
Hyperstructures, 51
Hypersurface, 2
Hypervolume preservation, 164, 167

IBM, 292, 312
IBM computers, 277, 282, 283, 286, 289, 292, 295, 296, 301, 305, 307, 308, 309
IBMOL
, 284, 289, 312
ICL computers, 296, 305
Ideal gas law, 180
Implicit method, 201
Information dimension, 260
Information matrix, 83
Inhibitor species, 206
Initial conditions, 110, 236
Initial value problems, 200
Insertion, 54
Internal bottlenecks, 163
Internal coordinates, 104
International Computers and Tabulators, 287
International Computers Limited, 287
International Journal of Quantum Chemistry
, vi
Intramolecular bottlenecks, 168
Intramolecular energy transfers, 120
Introns, 35
Invariant tori, 137, 167
Inversion, 27
Invertible map, 253
Iodate-arsenite reaction, 185, 189
Irrational approach, 75, 97
Isolas, 187
Isomerization, 159
Isomorphous replacement method, 48
Isosterism, 81
Iterative resynthesis, 96

Jacobian matrix, 194, 197, 199, 203, 207, 221, 230
Joint Academic Network, 300
Joint Network Team (JNT), 300
Journal of Chemical Information and Computer Sciences
, vii
Journal of Computational Chemistry
, vii
Journal of Molecular Graphics
, vii
Journal of Molecular Modeling
, v

KAM theorem, 119, 130, 131, 150
KAM tori, 131, 132, 138, 153, 158, 168
Kennard, O., 298
Keyboard, 275
Kinetic energy, 105, 122
Kinetic rate constants, 57
Kleier, D. A., viii
Knotted conformations, 38
Kollman, P. A., viii

Lack of Fit (LOF), 52
Lagrangian, 105
Lamarckian genetic algorithm, 32, 38
Landau theory, 245
Laplacian operator, 227
Latent property space, 78, 94
Lateral instabilities, 224
LCAO MO SCF, 282, 283, 289, 308
Lennard-Jones, J. E., 277
Libraries of compounds, 75, 76, 95
Life, 180
Ligand flexibility, 47
Ligand-protein docking, 62
Ligand-protein systems, 46
LiH, 290
Limit cycle, 198, 200, 237, 262
Limit cycle attractor, 199, 231, 233, 236, 244
Limit sets, 132
Linear stability analysis, 140, 143, 154, 155, 191, 192, 207
Linearized reactive island theory, 120, 158
Liouville's theorem, 164, 166
Lipophilicity, 79
Lipscomb, W. N., viii
Local filter, 48
Local gradient, 39
Local minima, 1, 14, 39, 43
Local minimization, 16
Local search, 11, 22, 24
Local stability, 190, 191
Local structure, 44
Log Ko/w, 82, 87
Logistic map, 238, 244
LOGKOW
, 79
Longuet-Higgins, C., 283, 290
Loop libraries, 45
Loop regions, 43, 45
Lyapunov dimension, 260, 264
Lyapunov exponent, 236, 253, 261, 262

MacroModel
, 39
Magnetic drum, 274, 276
Manodromy matrix, 143, 144
Mark computers, 274, 275, 276
Many-center integrals, 283
Map, 244
Mass screening, 75
Massachusetts Institute of Technology, 282
Master-slave arrangement, 33
Mating pool, 9
Maximum dissimilarity, 93
McWeeny, R., 294
Meeting Houses, 293, 301
Meiosis, 36
Melittin, 44
Mercury, 276, 286
Message passing, 33
Messy chromosome, 30
Messy genetic algorithm, 18, 30, 46, 65
Meteorology, 181, 235
Method of time delays, 259
Metropolis Monte Carlo, 38, 43, 59
Microcanonical ensemble, 103, 110
MICROMOL
, 311
Microscopic reaction dynamics, 116
MINDO
, 308
Minimum chemical distance, 51
Mitosis, 36
Mixed-mode oscillations, 254, 259
Mixed-mode route to chaos, 252
Mixed-mode states, 247, 257
MNDO
, 308
Mobius strip, 145, 163
Mode-mode coupling, 126, 150
Mode-mode energy transfer, 130, 132
Mode-mode resonance, 138
MOLCONN-X
, 79
Molecular connectivity indices, 87
Molecular design, viii, 53
Molecular docking, 46
Molecular dynamics (MD), 63, 102, 103, 108, 109, 231, 290, 301
Molecular graphics, viii
Molecular mechanics, viii
Molecular modeling, v, 37
Molecular motions, 115
Molecular phase space, 101
Molecular properties, 78
Molecular quantum chemistry, 276
Molecular similarity, 49, 78
Molecular simulations, viii
MOLECULE
, 296
Møller-Plesset (MP) theory, 303
Momentum, 104
Monte Carlo, 43, 44, 63, 301
MOPAC
, 46, 308
Morse potential, 123
Moskowitz, J., 284
Mulliken, R. S., 283
Multi-niche crowding, 56
Multidimensional scaling (MDS), 78
Multiple sequence alignments, 56
Multiple steady states, 182
Multiple variable systems, 193
Multistability, 182
MUNICH
, 285, 296
Murrell, J. N., 294
Mushrooms, 187
Mutation, 4, 6, 10, 19, 34, 47, 54
Mutation operator, 10, 31, 44, 53, 54
Mutation rate, 10, 15, 23, 35
Myoglobin, 45

N-map, 150
Naphthalene, 37
NAS 7000 computer, 309
National Institute for Research in Nuclear Science (NIRNS), 286
National Institutes of Health (NIH), 298
National Research and Development Corporation (NRDC), 272
National Research Council of Canada (NRCC), 285
Native structure, 44
Natural evolution, 3
Natural selection, 3, 9
Nelder-Mead simplex method, 38, 60
Nernst, W., 217
Networking, 299
Neural Net (NN), 55
Neural Network/Evolutionary Algorithm, 55
Newton-Raphson method, 201, 229
Newton's equations of motion, 103, 104, 108
Newton's method, 203
Next-return map, 233
Niche, 41, 55
Niching, 27
Nicotinamide adenine dinucleotide (NADH), 252
NMR, 291
NO2, 303
Noisy functions, 32
Nonchaotic systems, 236
Nonequilibrium thermodynamics, 179
Nonhomogeneous systems, 205
Nonlinear chemical kinetics models, 201
Nonlinear coupled system, 239
Nonlinear dissipative systems, 234
Nonlinear dynamical systems, 101, 117, 235
Nonlinear dynamics, 117, 119, 128, 177
Nonphysical solutions, 20
Nonstatistical effects, 101, 102
Normal forms, 190
Normally invariant hyperbolic manifold, 160
Norwegian Defence Research Establishment, 276
Nuclear coordinates, 103
Nuclear momenta, 103
Nuclear Overhauser effect (NOE), 49
Nuclear Structure Facility (NSF), 301
Numerical Algorithm Group (NAG), 291
Numerical Recipes
, 199

OCS, 120, 149
Octanol/water partition coefficient (Log Ko/w), 79
Off-line performance, 9
Offspring, 4
Olsen model, 265
One-point crossover, 26
Open chemical reactor, 180, 183
Open systems, 182, 206
Optimal control problem, 42
Optimality, 84
Optimization, 1, 37, 290
Order in chaos, 140
Order of schema, 19
Ordinary differential equation (ODE), 104, 191, 199
Oregonator, 228
Organization of matter, 81
Orion computer, 292
Oscillations, 195
Oscillatory systems, 206
Outcrossing, 37

Packet Assembler-Disassemblers (PADs), 300
Paging, 274
Paper tape, 274
Parallel computing, 33, 311
Parallel direct search, 39, 61
Parallel optimization, 2
Parameter values, 22
Partial differential equations (PDE), 226, 227
Partially matched crossover, 26
Particle-in-a-box model, 180
Pattern recognition, 311
Pattern search, 62
Penalty functions, 20, 21
Peptidases, 55
Peptoid libraries, 91, 95
Period doubling, 226, 238, 258
Period-four state, 239, 243
Period-one state, 239, 243
Period-two state, 239, 243
Periodic behavior, 238
Periodic orbit, 131, 132, 140
Periodic orbit dividing surface (PODS), 128, 150
Periodic oscillations, 183
Peroxidase-oxidase reaction, 249, 252
Pharmacophore, 49, 76, 83, 85, 94
Phase-locked behavior, 245, 247
Phase space, 102, 199, 231, 236
Phase space averages, 105
Phase space donut, 126
Phase space portraits, 232, 259
Phase space structures, 101
Phenotype, 6, 8, 35
Phospholene, 120, 156
PIG, 276
Pitchfork bifurcation, 193
Planar wave, 225
Plug boards, 274
Poincaré-Birkhoff theorem, 131
Poincaré integral invariants, 164, 165, 166
Poincaré maps, 119, 133, 134, 136, 137, 138, 141, 142, 147, 149, 153, 155, 164, 231, 233, 243
Poincaré sections, 231, 2324, 242, 254
Poincaré surface of section, 232
POLYATOM
, 284, 296
Polymer folding, 42
Polymers, 53
Pomona95
, 79
Pople, J. A., 285
Population convergence, 41
Population dynamics, 189, 190
Population size, 12, 22
Populations, 2, 6, 8
Positional scanning, 96
Potential energy, 104, 122
Potential energy functions, 58
Potential energy surface, 155
Predator-prey systems, 189
Prediction spectrum, 41
Predictor-corrector method, 230
Premature convergence, 20
Primary-1 back-reactors, 152, 154
Principal components analysis (PCA), 79
Programs, 65, 205
Prolog P
, 79
Propagating reaction-diffusion fronts, 188, 215, 216
Properties, 79
Property space, 76, 77, 78, 88
Protease inhibitors, 47
Protein conformation, 44
Protein crystallography, 48, 280, 281, 301, 311
Protein engineering, 43, 55
Protein flexibility, 47, 62
Protein NMR data analysis, 48
Protein sequences, 45, 55
Proteins, 7, 40
Pseudo-receptor, 50
Pseudopotential methods, 303
Punched cards, 274, 300
Punched tape, 300

QCPE
, 289
Quadratic autocatalysis fronts, 217, 222
Quadratic map, 238
Quantitative Structure-Activity Relationships
, vii
Quantitative structure-activity relationships (QSAR), v, 6, 12, 52, 84, 88, 89
Quantum chaos, 168
Quantum chemistry, 277, 285, 307
Quantum Chemistry Program Exchange (QCPE), 291
Quantum dynamics, 109, 168
Quantum mechanics, 105, 177
Quarks, 178
Quarterly News Letters
, 311
Quasi-steady-state assumption, 191
Quasiclassical simulations, 108
Quasiperiodic behavior, 119, 245
Quasiperiodic orbit, 160
Quasiperiodic states, 251
Quasiperiodic trapping, 102
Quasiperiodicity, 119, 168

Radius of gyration, 44
Ramachandran plots, 7
Random search, 38, 49, 59, 62
Rank-based selection, 24
Rank fitness, 24
Rate constant, 103, 112, 115, 185
Rational drug design, ix, 75
Reaction coordinate, 109, 156
Reaction-diffusion fronts, 215, 219
Reaction-diffusion models, 181, 214
Reaction-diffusion equations, 218, 223, 226
Reaction dynamics, 101, 281
Reaction rate, 103, 109, 156
Reactive islands, 120, 150, 152, 156, 157
Reactive motion, 123
Real-valued chromosomes, 31
Receptor interaction descriptors, 79, 81, 82
Reciprocal residence time, 186, 187, 188
Recrossing problem, 116
Reductionist philosophy, 177, 178, 179, 180
Redundant properties, 79
Regional Computer Centres, 297
Regression hypothesis, 113
Regular motion, 117
Regulator gene, 30
Reordering, 27
Replacement, 10, 25
Repulsive manifold, 145
Repulsive periodic orbit, 145
Resonance zone, 136, 137
Resonant dynamics, 130
Rice-Ramsperger-Kassel-Marcus (RRKM) theory, 102, 114
RNA, 48
Robb, M. A., 294
Rössler attractor, 238, 240, 244
Rotamer library, 40, 44, 48
Rotation number, 255
Roulette wheel selection, 9, 25, 32
Routes to chaos, 238
RTN scenario, 247
Runge-Kutta methods, 200, 201, 202, 240
Rutherford Appleton Laboratory (RAL), 292, 296
Rutherford High Energy Laboratory (RHEL), 286, 292, 295

Saddle point, 184
SAS
, 80
Scaffold, 75, 77, 87
Scalar processors, 306
Scaling, 32
Scattering theory, 290
Schema, 16
Schema theorem, 18, 19
Schnackenberg model, 211
Science Board, 293, 298, 306
Science Board Computing Committee (SBCC), 304, 310
Science Engineering Research Council (SERC), 298, 309, 310
Science Research Council (SRC), 285, 298, 309
Scoring functions, 89
Scroll waves, 230
Search keys, 80
Second-generation libraries, 88, 89
Secondary structure, 43
Segmented genetic algorithm, 44
Selection, 4, 9, 34
Self-organizing systems, 179
Self-similar features, 250
Separatrix, 124, 128, 136, 137, 138, 140, 146, 147, 149, 155, 162
Sequence alignment, 50
Shape descriptors, 79
Sharing operator, 48
Side chain conformations, 40, 44
SIGMA
(System for Integrated Genome Map Assembly), 55
Similarity, 77
Similarity matrix, 78
Simple genetic algorithm (SGA), 6, 11, 49
Simplex, 60, 62
Simulated annealing, 20, 38, 43, 49, 59, 62
Single-point crossover, 10, 25
Slater, J. C., 283
Slater orbitals, 283
SMILES, 54
Sparse matrix driven method, 41
Spatiotemporal patterns, 180, 206, 214
Spectral curve fitting, 57
Spectral simulations, 281, 291
Spectroscopy, 168
Spin-glass Hamiltonian, 48
Spiral waves, 230
Spiraling trajectories, 198
Split/mix solid phase synthesis, 96
Spontaneous patterns, 205
Spruce budworm, 189
Stability analysis, 190, 234, 237, 244
Stability manifolds, 137
Stable Manifold theorem, 137, 150, 163
Stable manifolds, 132, 237
Stable nodes, 184
Standard homoclinic/heteroclinic tangle, 148, 150
State transition matrix, 42
Stationary fitness functions, 29
Stationary state, 182
Statistical mechanics, 105, 180, 281
Steady state, 184, 186, 187, 188, 207, 209
Steady state attractor, 199, 231, 233, 236
Steady state genetic algorithm, 56
Steady state replacement, 25
Step function selection, 25
Steric fitting, 63
Stiff equations, 199, 201, 239
Stiffly stable algorithm, 202
Stilbene, 120, 157
Stochastic web, 167
Stored program machine, 273
Strange attractors, 231, 236
Structure-activity relationship (SAR), 76, 83, 92
Structure-based drug design, ix, 89
Structure-based library design, 89
Substituent properties, 79, 88
Substituents, 77, 84
Substructural fragments, 93, 95
Substructure searching, 51
Superdelocalizability, 81
Surface of section, 119, 133, 135, 137, 150, 151, 164, 165, 232
Sutcliffe, B. T., 294, 296, 303
SYBYL
, 39, 61
Symplectic geometry, 164
Synchrotron Radiation Source, 301
Synthesis, 96
Synthetic chemistry, vi
Systematic search, 61, 63

Tanimoto coefficients, 78, 79, 80, 81, 93
Target-focused libraries, 76
Taylor-Couette flow, 246
Taylor series expansion, 192, 194, 201, 207
Telecommunications, 299
Template diversity, 87
THEOCHEM
, vi
Theoretica Chemica Acta
, vi
Theoretical chemistry, 177
Theoretical physics, 180
Thermionic valves, 273
Thermodynamic equilibrium, 182, 187
Thermodynamic functions, 105
Thermolysin inhibitors, 46
Three-dimensional torus, 245
Three-point pharmacophores, 95
Time-reversal symmetry, 142
TITAN computer, 290
Topological equivalence of portraits, 259
Topological indices, 79
Topological shape, 82
Topology, 126, 131
Torsional isomerization, 120
Torus, 126
Torus attractor, 244, 245, 246, 253
Tournament selection, 25, 31, 47
Trajectories, 103, 104, 236
Transition points, 186
Transition state, 102, 109, 114, 116, 122, 151, 155, 156, 161, 163
Transitor, 280
Transmission coefficient, 158
Trapezoidal algorithm, 201
Traveling salesman problem, 26
Tree-pruning algorithms, 61
Trichloroethane, 121
Turbulence, 245
Turbulent fluid flow, 245
Turing, A., 181, 273, 277
Turing bifurcation, 206, 212, 213
Turing patterns, 181, 205
Turnstiles, 147
Two-dimensional torus, 245
Two-point crossover, 25
Two-state isomerization, 127

Unbiased D-optimal library, 90
Uncoupled isomerization dynamics, 121
Uniform crossover, 26
Unimolecular decomposition, 156
Unimolecular exchange, 120
Unimolecular isomerization, 110, 119, 120
United Kingdom, 271
United States, 274, 312
Univac 1103 computer, 282
Universal laws, 179, 181
University Grants Committee (UGC), 272
Unstable focus, 198, 245
Unstable manifolds, 132, 237
Unstable periodic orbits, 243
Usenet group, 65

Vague tori, 120
Valence bond theories, 298, 306
Variance/covariance matrix, 83
Vector processors, 303, 304, 306
Vibrational energy transfer, 120
Video display units, 299
Virtual storage, 274

Whirlwind, 282
Williams tube, 274
Winding number, 248, 255
Wolf algorithm, 263
Working group, 294
World Wide Web (WWW), x
Wrinkled torus, 253, 257

X-ray crystallography, 48, 277, 281

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