Index

activated complex theory, 8 activity coefficients, 8 AND gate, 37, 43 Arrhenius equation, 7–8 autocatalysis, 125 autocatalytic species, 132 autocorrelation function, 25

Belousov–Zhabotinsky (BZ) reaction, 125–127

bifurcation analysis, 129–131, 129, 130 bifurcation diagrams, 115, 143–147, 145, 146 binary coding, 104–105

biochemical reaction network (BRN), 40 bioinformatics, 207–209

Bayesian networks, 215–220, 216, 217, 218, 219

Boolean networks, 211–213, 213 clustering, 208, 209

correlation metric construction for genetic networks, 213–215, 214, 215

linearization, 209–210, 210

modeling reaction mechanisms, 210–211,

212

other approaches, 220–221

bistable reaction systems and bistable electronic switches, 37–38

blue fluorescent protein (BFP), 23

capillary electrophoresis (CE), 13–15 capillary isoelectric focusing (CIEF), 14 capillary zone electrophoresis (CZE), 14 catalyst, definition, 3

causal connectivity, definition, 3 cellular dynamics, 12

chemical neurons, 34–37, 36 chlorite–iodide reaction, 129–131, 129, 130,

160

bifurcation diagrams, 163–164, 163 concentration shift destabilization,

161–162, 162, 162

concentration shift regulation, 161, 161 model, 164–165, 165

phase shift of oscillations, 164 qualitative pulsed species response,

160–161, 161 classical identification, 4–6

complex systems, deducing reaction mechanisms, 2

224 INDEX

computations by macroscopic kinetic systems, 34

chemical neurons and logic gates, 34–37, 36 computational functions, 40–44, 41 implementation of computers, 37–40,

38, 39 concentration

correlation function method, 2 relative change, 47

stationary state, 47

continuous-flow stirred tank reactor (CSTR), 37–39, 38, 39, 59

control, definition, 3 controllability, 5 Coomassie Blue stain, 21

correlation metric construction (CMC) experimental test, 87–96, 88, 90

matrix summary of distance matrix, 92 MDS diagram, 93

time-lagged correlation function, 91 genetic networks, 213–215, 214, 215 theory of statistical construction of reaction

mechanisms, 65–85, 68, 72, 77, 78, 81

cross-correlation function, 25 cross-shaped diagram, 131, 144 cyan fluorescent protein (CFP), 23 cycle species, 132

cyclic pathways, 135–136 cyclin-dependent kinase (CDK), 212

density estimation

entropy metric construction (EMC), 97–102, 100, 101

deterministic kinetics, 7–8 disappearance processes, 193 disordered kinetics, 9

DNA microarrays, 18–20, 19 Drazer–Zanette experiment, 176–180, 181

Easterby’s equation, 187 electro-osmotic flow (EOF), 13–14 electrospray ionization (ESI), 16 elementary reaction, definition, 3 entropy, 98

entropy metric construction (EMC), 97–102,

100, 101

entropy reduction method (ERM), 102 enzyme binding and rate coefficients (EBR),

114–115 exit species, 132

feedback mechanisms, 125 feedback species, 133 fluctuations, 9

fluorescence localization after photobleaching (FLAP), 24

fluorescence loss in photobleaching (FLIP), 24 fluorescence recovery after photobleaching

(FRAP), 24 fluorescent dyes, 21 fluorescent imaging, 23

fluorescence correlation spectroscopy (FCS), 25–26, 25

fluorescence resonance energy transfer (FRET), 26–27

fluorescence speckle microscopy (FSM), 24 future trends, 27

photobleaching and photoactivation, 23–24 total internal reflection fluorescence

microscopy (TIRFM), 25

Fourier Transform Ion Cyclotron Resonance (FT-ICR) MS, 17

fructose 6-phosphate/fructose 1,6-biphosphate cycle, 40–43, 42

gas chromatography-mass spectrometry (GC-MS), 13

genetic algorithm method, 2

genetic algorithms (GAs), 104–105, 122 basic techniques

crossover, 105 elitism, 105 mutation, 105

roulette wheel selection, 105 termination, 106

evolutionary development of biochemical oscillatory reaction mechanisms, 112–118, 117, 118

enzyme binding constants, 114

flux regulation selection, 106–112, 106 limiting network diagrams, 111 noncompetitive binding, 107

systematic determination of reaction mechanism and rate coefficients, 119–122

genome, 207 gluconeogenesis, 43 glycolysis, 4, 42–43, 113

experimental test of correlation metric construction (CMC), 87–96, 88, 90

matrix summary of distance matrix, 92 MDS diagram, 93

time-lagged correlation function, 91

experimental test of pulse perturbation method, 58–64, 59, 60, 61, 63

pathway, 53–56, 54, 55, 56 green fluorescent protein (GFP), 23 Green functions, 185, 193

high-performance anion-exchange chromatography (HPAEC), 12, 13

high-pressure liquid chromatography (HPLC), 12–13

proteome analysis, 21

Hopf bifurcation, 129, 130, 131, 143 horseshoe effect, 83 hydrophilic-interaction chromatography

(HILIC), 13

input negative feedback, 137 inverse self-regulation, 142

iodate–arsenous acid reaction, 37, 38, 39 ion trap mass analysers, 17

ionic strength, 8 isobaric tags, 22

isotope-coded affinity tags (ICAT), 22

Jacobian matrix elements (JMEs), 128–129

Kalman filtering, 5 kinetic processes

disordered kinetics, 9 fluctuations, 9

macroscopic, deterministic kinetics, 7–8

Langmuir adsorption isotherms, 176

lifetime distributions of species, 171–173, 205 response experiments, 173–182

errors, 192–197, 194, 195 LISREL, 5

logic gates, 34–37, 36, 40–43, 42

marked species, 198 mass action law, 46

mass action rate expressions, 7 mass spectrometry (MS)

principles and applications, 15–16 detectors, 17–18

HPLC detectors, 13 mass analyzers, 16–17

mass-to-charge ratio (m/z) of ions, 16 matrix-assisted laser desorption/ionization

(MALDI), 16 metabolome, 12 methodologies, 11, 27

INDEX 225

fluorescent imaging, 23–27 genome-wide analyses of mRNA and

proteins, 18

DNA microarrays, 18–20, 19 proteome analysis, 20–23, 22 mass spectrometry (MS), 15–16

detectors, 17–18

mass analyzers, 16–17

metabolite concentration measurements, 11–12

capillary electrophoresis (CE), 13–15, 15 high-pressure liquid chromatography

(HPLC), 12–13 metric, requirements, 98

micellar electrokinetic capillary chromatography (MECC), 14

molality, 8 mRNA, 207

linearization, 209–210, 210 multidimensional scaling (MDS), 73–82, 75,

76, 78, 81 glycolysis, 93

multivariate systems, 5–6

NAND gate, 66, 78

network performance evaluation, 109–110 neural networks, 40

NFT mechanism, 119–120 nonlinear systems, 5 NOR gate, 42

normal self-regulation, 142 normalized correlation functions, 67 Nyquist critical frequency, 6

observability, 5 OR gate, 43

oscillatory reactions, 2, 125–127 concepts and theoretical constructs,

127–128

bifurcation analysis, 129–131, 129, 130 categorization of oscillatory reaction,

136–137

Jacobian matrix elements (JMEs), 128–129

role of species, 131–133

stoichiometric network analysis (SNA), 133–136, 134, 136

deduction of mechanism examples, 151 chlorite–iodide reaction, 160–165 peroxidase–oxidase (PO) reaction,

151–160, 152

226 INDEX

oscillatory reactions (continued) experiments providing mechanism

information, 138 amplitude relations, 138, 140

bifurcation diagrams, 143–147, 145, 146 characterization of species, 138, 139 concentration shift destabilization, 143 concentration shift regulation, 141–142 delay experiments, 148

external periodic perturbation, 150 other methods, 151

phase relations, 139–141

phase response experiments, 149–150 pulsed species response, 147–148, 147 quenching, 148–149

stabilization of unstable steady state, 150 limits of stoichiometric network analysis,

166

output negative feedback, 137

ozone, formation and decomposition by light in upper atmosphere, 2

pair correlation function, 97 pair probability distribution, 99 parallel computing, 40

pattern recognition, 39 pentose cycle, 4

peroxidase–oxidase (PO) reaction, 151–152, 156–157, 157

concentration shift destabilization, 154–155, 155

concentration shift regulation, 153–154,

154, 154

model, 157–160, 158, 159

phase shifts of oscillations, 152, 153 qualitative pulsed species response, 155,

155

quench experiments, 156, 156

relative amplitudes of oscillations, 152, 153 phase response curve (PRC), 149

phase transition curve (PTC), 149 phenotype, 11 phosphorylation/dephosphorylation cycle, 41 photoactivation, 23–24

photobleaching, 23–24 Polanyi relations, 177

polyacrylamide gel electrophoresis, 21 primary salt effect, 8

proteome analysis, 20–23, 22 pulse method, 2

pulse perturbations

experimental test, 58–64, 59, 60, 61, 63 glycolytic pathway, 53–56, 54, 55, 56 theory, 46–53, 47, 48, 50, 51, 52

quadrupole mass analyzers, 16 quenching, 148–149

rate coefficients, 8 reachability, 5

reaction–diffusion systems, 197–204 reaction mechanisms, definition, 3 reaction pathway, definition, 3 reactions, 1

recovery species, 133

red fluorescent protein (RFP), 23 relative change in concentration, 47 replication processes, 193 reverse-phase (RP) HPLC, 13 RNA, 207. See also mRNA

saddle-node bifurcations, 130 selected ion monitoring (SIM), 16 SEPATH, 5

sign-symbolic shift matrix, 139, 140, 141, 142 silver staining, 21

single nucleotide polymorphisms (SNP), 18 stationary state concentrations, 47 statistical construction of reaction

mechanisms, 65–85, 68, 72, 77, 78, 81 stochastic elements in reactions, 5 stoichiometric equations, 1

stoichiometric network analysis (SNA), 131, 133–136, 134, 136

limits, 166

susceptibility functions, 185

time-lagged correlation function, 67, 69, 70, 73

glycolysis, 91

time-of-flight (TOF) mass analyzers, 16–17 total internal reflection fluorescence

microscopy (TIRFM), 25 tracers, 170

transformation processes, 193 transit time distributions, 182–188

extracting kinetic information from experimental data, 188–192

Turing machines, 40

yellow fluorescent protein (YFP), 23

Zeldovich–Roginskii model, 178