Topology in Molecular Biology

238 Index

linking number, 9, 10, 24, 25, 43, 45, 52,
103, 179
Gauss linking number, 184
links, 23, 25–27, 35, 69, 71, 73, 103, 111,
112, 114

Massey product, 183
membran, 185
mirror images, 71, 97
Morse-Novikov theory, 198

packing, 215
close packing, 148
close-packing, 148, 150, 157
sphere packing, 149
palindrome equivalence, 93
Pell’s equation, 161
Polypeptide chain topology, 147, 148,
150–152
polytop{3,3,5}, 150, 151, 153, 155
proteins
protein folding, 128
Secondary structure, 129, 130, 135,
140, 147
Structural Classification, 129

quasicrystal, 149, 150

rational approximants, 150, 158

rational convergents, 150, 159

similarity

sequence similarity, 135

structure similarity, 155

snub cube, 152, 153

solvmanifold, 199

Structure prediction, 127, 128, 143

supercoiled DNA, 184

tangles, 71

2-tangles, 71

alternating tangles, 81

classification of rational tangles, 77

rational tangles, 69, 70, 72, 73, 113,

114

the tangle model, 69

two-tangles, 70

twist grain boundaries, 157, 161

Whitehead link, 182

winding number, 152

Witten’s deformation, 195

wormlike chain, 6–8, 26, 29, 30

wormlike chain,, 31

writhing number, 184