Topology in Molecular Biology

Index

Aharonov-Bohm experiment, 192
Alexander duality, 182
Alexander polynomials, 34, 35, 37
alternating knots, 74, 92, 112, 113
amino acid, 127, 128, 132, 135, 136,
147–153, 157
Archimedean lattice, 154, 159
arrangement of the strands, 129–131,
136, 137, 139–141

beta sheet, 130, 137, 139–141, 143
biopolymer, 44, 45
Borromean rings, 182

chirality, 26, 37, 97, 98, 111, 123, 148,
150, 153
coincidence site lattice, 156, 161
collagen, 147, 149–151, 159
conductance, 71, 81, 92
connective tissue, 147
continued fraction, 69–71, 77, 78, 101,
160
continued fractions, 78–80
crystallography, 127
cuts
special cuts, 95, 96

Dirac monolope, 191
DNA conformations, 18, 39
DNA conformations., 23
DNA effective diameter, 28, 32
DNA model, 23, 26, 29, 46
DNA recombination, 16, 19, 69, 71, 105,
108

DNA supercoiling, 14, 23, 31, 42, 45

DNA topology, 3, 4, 24, 43, 47, 57

DNA torsional rigidity, 29, 32

fibration, 151, 152

Hopf fibration, 177

fibril

collagen, 148, 157, 162

flip, 75

flypes, 74, 79

Formula Cˇalugˇareanu, 184, 185

geometrical flustration, 151, 162

glycine, 148

helix

Boedijk-Coxeter helix, 149

Coxeter helix, 150, 151

hidden Markov models, 134, 144

Hopf fibration

fibration, 149–151, 153

Hopf invariant, 180, 181

Hopf tori, 186

hydrophobic conservation, 132

immunoglobulin, 131

immunoglobulin fold, 131

intersection number, 179

knots, 11, 12, 16, 31, 33–35, 69, 71, 73,

74, 77, 111, 112, 118, 119

rational knots, 69, 77, 92, 114, 115

Lie algebra cohomology, 202